linuxforhealth/fhir

The LinuxForHealth FHIR® Server and related projects

LinuxForHealth FHIR Server

The LinuxForHealth FHIR® Server (formerly the IBM® FHIR® Server) is a modular Java implementation of the HL7 FHIR specification that supports versions R4 and R4B with a focus on performance and configurability.

For a detailed description of FHIR conformance, see https://linuxforhealth.github.io/FHIR/Conformance.

The server is available in the following forms:

• a web application archive (war)
• a zip file with installation script
• a Linux container image from GitHub Packages
• a helm chart registered on ArtifactHub

Running the server

Guides for configuring, operating, and extending the LinuxForHealth FHIR Server are available from https://linuxforhealth.github.io/FHIR/guides/FHIRServerUsersGuide.

From the zip installer

Download the fhir-persistence-schema and fhir-install assets from the Releases tab and follow the instructions from the User's Guide to:

1. Use fhir-persistence-schema-VERSION-cli.jar to deploy the schema.
2. Unzip, install, and configure the server.

From the container image

Quickstart:

docker run -p 9443:9443 -e BOOTSTRAP_DB=true ghcr.io/linuxforhealth/fhir-server

Note:

1. The Docker image ghcr.io/linuxforhealth/fhir-schematool is an early technology preview and is experimental.
2. The Docker image ghcr.io/linuxforhealth/fhir-bucket-tool is an early technology preview and is experimental.
3. The Docker image ghcr.io/linuxforhealth/fhir-term-loader is an early technology preview and is experimental.

From the helm chart

Quickstart:

helm repo add linuxforhealth https://linuxforhealth.github.io/lfh-helm
export POSTGRES_PASSWORD=$(openssl rand -hex 20)
helm upgrade --install --render-subchart-notes fhir-server linuxforhealth/fhir-server --set postgresql.postgresqlPassword=${POSTGRES_PASSWORD} --set ingress.hostname=example.com --set 'ingress.tls[0].secretName=cluster-tls-secret'

See https://artifacthub.io/packages/helm/linuxforhealth/fhir-server for more information.

Building with the LinuxForHealth FHIR Modules

Each of the LinuxForHealth FHIR Server modules are published to Maven Central under org.linuxforhealth.fhir.

To use the artifacts from a Maven project, declare the dependencies. For example, to use our visitable, thread-safe FHIR object model (including our high-performance parsers and generators), declare a dependency on the fhir-model module:

...
<dependencies>
    <dependency>
      <groupId>org.linuxforhealth.fhir</groupId>
      <artifactId>fhir-model</artifactId>
      <version>${fhir.version}</version>
    </dependency>
    ...

LinuxForHealth FHIR modules

The LinuxForHealth FHIR Server is modular and extensible. The following tables provide an overview of all the modules, along with an indicator of the stability of the Java APIs defined in each module. This indicator is only applicable to the direct usage of the modules, not for usage of the LinuxForHealth FHIR Server as a whole.

Core

Module	Description	Java API-stable
fhir-parent	The parent project for all projects which make up the LinuxForHealth FHIR Server	false
fhir-core	Core helpers and utilities	false
fhir-cache	Cache-related helpers and utilities	false

Model and Profile Support

Module	Description	Java API-stable
fhir-model	An object model generated from the FHIR R4B specification and corresponding parsers and generators for XML and JSON	true
fhir-registry	A resource registry and registry provider interfaces for extending the registry	false
term/fhir-term	A terminology service provider interface with a default implementation that implements terminology services from fully-defined CodeSystems in the registry	false
term/fhir-term-graph	An expermental terminology service provider that implements terminology services using JanusGraph	false
term/fhir-term-graph-loader	Utilities to populate the fhir-term-graph JanusGraph with concepts	false
term/fhir-term-remote	A terminology service provider that connects to an external service using a REST client to access code system content	false
fhir-profile	Helper methods for validating ValueSet membership and Profile conformance	false
fhir-path	An implementation of version 2.0.0 of the FHIRPath specification	false
fhir-validation	Validation utility for validating resource instances against the base specification and configured profiles	false
conformance/fhir-core-r4	Conformance artifacts for HL7 FHIR version 4.0.1	false
conformance/fhir-core-r4b	Conformance artifacts for HL7 FHIR version 4.3.0	false
conformance/fhir-hl7-terminology	CodeSystems and ValueSets from HL7 Terminology (THO) version 3.1.0	false
conformance/fhir-ig-us-core	Packaging the US Core Implementation Guide for the LinuxForHealth FHIR registry	false
conformance/fhir-ig-mcode	Packaging the minimal Common Oncology Data Elements for the LinuxForHealth FHIR registry	false
conformance/fhir-ig-carin-bb	Packaging the Consumer-Directed Payer Data Exchange Guide for the LinuxForHealth FHIR registry	false
conformance/fhir-ig-davinci-pdex	Packaging the Da Vinci Payer Data Exchange (PDEX) Implementation Guide for the LinuxForHealth FHIR registry	false
conformance/fhir-ig-davinci-hrex	Packaging the Da Vinci Health Record Exchange (HREX) Implementation Guide for the LinuxForHealth FHIR registry	false
conformance/fhir-ig-davinci-pdex-plan-net	Packaging the Da Vinci Payer Data Exchange (PDEX) Plan Net Implementation Guide for the LinuxForHealth FHIR registry	false
conformance/fhir-ig-davinci-pdex-formulary	Packaging the Da Vinci Payer Data Exchange (PDex) US Drug Formulary Implementation Guide for the LinuxForHealth FHIR registry	false

Server

Module	Description	Java API-stable
fhir-config	Configuration property definitions and helpers for working with the fhir-server-config.json config files and multi-tenancy	false
fhir-audit	Audit-related interfaces and implementations including 1) a No-op AuditLogService and 2) an AuditLogService that writes audit events to Apache Kafka in the Cloud Auditing Data Federation (CADF) JSON format	false
fhir-search	Utilities for working with the FHIR search specification	false
fhir-persistence	Interfaces, helpers, and tests for implementing a persistence layer for the server	false
fhir-persistence-jdbc	A relational FHIRPersistence implementation that uses JDBC to store and query FHIR resources	false
fhir-persistence-cos	Decorates the fhir-persistence-jdbc module with the ability to offload payload storage to IBM Cloud Object Storage experimental	false
fhir-persistence-cassandra	Decorates the fhir-persistence-jdbc module with the ability to offload payload storage to Cassandra experimental	false
fhir-persistence-blob	Decorates the fhir-persistence-jdbc module with the ability to offload payload storage to Azure Blob experimental	false
fhir-provider	JAX-RS Providers for FHIR XML and JSON and related patch formats	false
fhir-server	JAX-RS resources and related classes for implementing the FHIR REST API and extended operations	false
fhir-server-webapp	A web application that packages the fhir-server with a set of built-in extended operations	false
fhir-server-test	End-to-end integration tests for testing a running server	false
fhir-smart	An interceptor that provides SMART-on-FHIR authorization policy enforcement	false

Extended Operations

Module	Description	Java API-stable
fhir-operation-test	Sample operations for testing Extended Operations as describe at https://hl7.org/fhir/R4B/operations.html	false
fhir-operation-bulkdata	$import and $export implementations which translate bulk data requests into JSR352 Java Batch jobs	false
fhir-bulkdata-webapp	Standalone web application for serving bulk import and export requests via JSR352 Java Batch jobs	false
fhir-operation-convert	A limited implementation of the FHIR $convert operation, able to convert between JSON and XML but not between FHIR versions	false
fhir-operation-document	Basic support for the Composition $document operation defined at https://hl7.org/fhir/R4B/operation-composition-document.html	false
fhir-operation-healthcheck	The $healthcheck operation checks for a valid connection to the database and returns the server status	false
fhir-operation-term	Terminology service operations which use the default fhir-term TerminologyServiceProvider to implement $expand, $lookup, $subsumes, $closure, $validate and $translate	false
fhir-operation-term-cache	Add-on module that provides operations for clearing the terminology subsystem caches for non-production scenarios	false
fhir-operation-validate	An implementation of the FHIR resource $validate operation	false
fhir-operation-everything	An implementation of the FHIR patient $everything operation	false
fhir-operation-erase	A hard delete operation for resource instances referred to as the $erase operation. See the README.md	false
fhir-operation-member-match	An extensible framework and reference implementation for Davinci HREX $member-match using the default IBM FHIR Server. See the README.md experimental	false

Client

Module	Description	Java API-stable
fhir-client	A FHIR Client that re-uses the LinuxForHealth FHIR Server model and its JAX-RS Providers	false

Clinical Quality

Module	Description	Java API-stable
cql/fhir-cql	Foundation classes for implementing the CQL Engine backend in IBM FHIR Server	false
cql/fhir-cql-rest	REST Client-based implementation of CQL Engine backend	false
cql/fhir-cql-server	Internal API-based implementation of CQL Engine backend	false
cql/fhir-quality-measure	FHIR Quality Measure evaluation logic	false
cql/operation/fhir-operation-cpg	Optional module that implements CQL operations	false
cql/operation/fhir-operation-cqf	Optional module that implements CQF operation	false
cql/operation/fhir-operation-apply	A naive implementation of the $apply operation defined at https://hl7.org/fhir/R4B/operation-activitydefinition-apply.html	false

Tools and Utilities

Module	Description	Java API-stable
fhir-tools	Code generation tools and logic for generating the FHIR object model, XML and JSON parsers, and the DefaultVisitor base class	false
fhir-database-utils	Generic database utilities for working with Apache Derby and PostgreSQL relational database management systems	false
fhir-examples-generator	A utility for generating resource examples which range from minimal (only required fields) to complete (every field present)	false
fhir-examples	A set of FHIR resource examples including 1) all examples from the FHIR Specification 2) a set of generated examples for test purposes	false
fhir-swagger-generator	Utilities for generating Swagger 2.0 and OpenAPI 3.0 definitions for a subset of the FHIR HTTP interface	false
fhir-openapi	A web application that provides a simplified OpenAPI 3.0 definition of the FHIR HTTP interface	false
fhir-install	Packaging and installation scripts for creating the fhir-distribution zip and the corresponding IBM FHIR Server Docker image	false
fhir-benchmark	Java Microbenchmark Harness (JMH) tests for measuring read/write/validation performance for the LinuxForHealth FHIR Server and the HL7 FHIR Java Reference Implementation	false
fhir-bucket	Scans cloud object storage buckets and uploads data using the FHIR REST API	false
fhir-persistence-schema	Classes for deploying and updating the LinuxForHealth FHIR Server relational database schema	false
fhir-persistence-cassandra-app	CLI utility application supporting payload storage to Cassandra experimental	false

Contributing to the LinuxForHealth FHIR Server

The LinuxForHealth FHIR Server is under active development. To help develop the server, clone or download the project and build it using Maven. See Setting up for development for more information.

See CONTRIBUTING.md for contributing your changes back to the project.

See CODE_OF_CONDUCT.md for code of conduct.

License

The LinuxForHealth FHIR Server and its corresponding modules are licensed under the Apache 2.0 license. The full license text is available at 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 at https://ibm.com/trademark.

fhir's Issues

DB2 stored procedure resource files have no content after copyright update

Describe the bug
DB2 stored procedure resource files have no content after copyright update.

To Reproduce
Try to deploy the schema.

Expected behavior
Schema should deploy successfully.

Additional context
N/A

Warning in `fhir-persistence-jdbc` is reported in the build.

Warning in fhir-persistence-jdbc is reported in the build.

Aug 30, 2019 2:31:12 PM com.ibm.watson.health.fhir.search.parameters.ParametersUtil populateSearchParameterMapFromStreamByFormat
WARNING: Error condition reading the FHIR Bundle of Search Parameters -> from_stream

SwaggerGenerator generates repeat parameters for global search parameters

Describe the bug
Currently, the generator creates parameters like this:

        "/RiskAssessment": {
            "get": {
                "tags": [
                    "RiskAssessment"
                ],
                "summary": "Search for RiskAssessment resources",
                "operationId": "searchRiskAssessment",
                "produces": [
                    "application/fhir+json"
                ],
                "parameters": [
                    {
                        "$ref": "#/parameters/_idParam"
                    },
                    ...
                    {
                        "$ref": "#/parameters/_idParam"
                    },

To Reproduce
Run FHIRSwaggerGenerator for search operations

Additional context
We recently changed the behavior of FHIRUtil.getSearchParameters so that it will return all the search parameters for a given resource type, including the ones inhereted from the generic Resource definition.
We still need to document that change (or revert it), but for now we just need to fix the generator.

Swagger Issues

The FHIRSwaggerGenerator for R4 still has some issues:

• looks for XMLElement annotation even though we don't use that any more
• only adds inhereted properties when the parent is a resource
• misses all enum due to using wrong delimiter for nested classes
• missing logic for handling Boolean
• choice elements get serialized without their typeSuffices
• object definitions are no longer scoped by their container classes

Update docs/FHIRServerUsersGuide.md for R4

FHIRServerUserGuide is where we document how to download, install, and run the Watson Health FHIR Server. This needs a serious overhaul for the R4 server.

Add bulkimportexport javabatch war to the distribution package

Enhance BulkExport to be able to support multiple resource Types

We need to figure out a way to support multiple resource types inside the javabatch job or we will have to ask the operation codes to send multiple job requests - one for each resource type and then consolidate the results.

Enable Travis for the FHIR Repository

Enable Travis for the FHIR Repository

Create .travis.yml

###############################################################################
# (C) Copyright IBM Corp. 2019
#
# SPDX-License-Identifier: Apache-2.0
###############################################################################

# Notes: 
# SKIPPING BUILD via Travis: 
# To skip the build use: 
# [skip <KEYWORD>]
# ci, travis, travis ci, travis-ci, or travisci
# Example: [skip travis] Update README

dist: xenial
sudo: false

language: java

# use Open JDK 8
jdk:
  - openjdk8

install:
  - java -version

matrix: 
  fast_finish: true

# Using a depth of false, we don't really modify git. 
git:
  depth: false
  quiet: true
  submodules: false

before_install: 
  - echo "MAVEN_OPTS='-Xmx2G -Xms1G -XX:MaxPermSize=512m -Djava.awt.headless=true -B'" > ~/.mavenrc

# Generate the VERSION - TRAVIS_BUILD_ID
# fhir-parent-it = Integration test
script: 
  - env
  - df
  - ulimit -a
  # fhir-tools - installs the generator
  - "mvn -f fhir-tools/pom.xml -B -P jenkins clean install -Dmaven.javadoc.skip=true"
  # fhir-examples = Exampes Data
  - "mvn -f fhir-examples/pom.xml -B -P jenkins clean install -Dmaven.javadoc.skip=true"
  # fhir-parent-ut = Unit Test
  - "mvn  -f fhir-parent/pom.xml -B -P jenkins clean install -Dcom.ibm.watsonhealth.fhir.model.spec.test.R4ExamplesDriver.testType=MINIMAL"

# cache the build files
cache:
  directories:
  - $HOME/.m2

notifications:
  email:
    recipients:
      - [email protected], [email protected]
    on_success: never # default: change
    on_failure: always # default: always  

Update ci/license/issuemanagement

Uses tag-release on push tag

Changes the mvn version (does the modification on the tag)

Travis.txt

ci for push build

ci for pr build

ci for tag build and release

Protect Branches

Update travis / bintray

we could do something like this...
git log <PRIOR_TAG>...<CURRENT_TAG> --name-only - if files changed since prior, then build the project, and release only the files which match the name changes

Merge bulkimportexport project to bulkimportexport-webapp project

As parting of our effort to reduce the total number of projects.

Bulkexport enhancement to support patient-export

The current export javabatch can only support the system level export of the spec.

We need to support patient export - export all patients' related resources.
https://build.fhir.org/ig/HL7/bulk-data/OperationDefinition-patient-export.html

Steps

1. Update the API $export Operation to accept the submission pattern from client for patient export with parameters:
   (1) -since (optional, if without, then export for all patient)
   (2) -format (optional, only support ndjson)
   (3) -resourceTypes (optional, if no resource Type, then the job will export all resourcetypes for patient)

2. Update the API $export Operation to call the patient export java batch job and pass in the parameters.

3. Create new java batch job for patient export
   (1) Take the parameters from patient export operation.
   (2) Construct the to-be-exported resource types - resource types parsed from the passed-in parameter or all compartment resource types of Patient.
   (3) For each resource type
   (a) Search and get a page of patients, for each found patient:
   -- compartment search using patient id to get the resources.
   -- write the found resources into buffer stream.
   (b) If checkpoint satisfied, then write the buffered resources to COS bucket and append the exported file info to batch job exit status.
   checkpoint algorithm: page of patients per exported file or by file size.
   (4) After all resource types are processed, exit the batch job.

4. Update the API $export Operation to parse the job exit status and construct links of exported resource type files and response to client.

Extra EAR projects are created needlessly on Maven Project import

Extra EAR projects are created needlessly on Maven Project import

Refactor $apply for PlanDefinition/CarePlan

Refactor $apply for PlanDefinition/CarePlan based on Feedback

• Create sample using Obesity Assessment Protocol where there is a measure of BMI http://hl7.org/fhir/plandefinition-protocol-example.json.html
• Address comments from Lee - #42

Enhance JavaBatch to be able to import from one or more cos objects with name started with certain string.

Update docs/Conformance.md for R4

Conformance.md is where we document our conformance to the FHIR DSTU2 specification. We need to update that to cover where we're at on the R4 implementation.

Test bulkexportimport javabatch job using Amazon s3

This will verify if the javabatch bulkexportimport job is compatible with Amazon S3 or not. if not, then make necessary code changes as needed.

Bulkexport group-export for members (not characteristic-based)

we need to support group-export per the spec.

https://build.fhir.org/ig/HL7/bulk-data/OperationDefinition-group-export.html

Steps

1. Update the API $export Operation to accept the submission pattern from client for patient export with parameters:
   (1) -since (optional, if without, then export for all patient)
   (2) -format (optional, only support ndjson)
   (3) -resourceTypes (optional, if no resource Type, then the job will export all resourcetypes for patient)
   (4) -group (mandatory)

2. Update the API $export Operation to call the group export java batch job and pass in the parameters.

3. Create new java batch job for group export
   (1) Take the parameters from patient export operation.
   (2) Construct the to-be-exported resource types - resource types parsed from the passed-in parameter or all compartment resource types of Patient.
   (3) For each resource type
   (a) Search and get the group via /Group/grpID.
   (b) get one page of patients from the group member, and for each found patient:
   -- compartment search using patient id to get the resources.
   -- write the found resources into buffer stream.
   (c) If checkpoint satisfied, then write the buffered resources to COS bucket and append the exported file info to batch job exit status.
   checkpoint algorithm: page of patients per exported file or by file size.
   (4) After all resource types are processed, exit the batch job.

4. Update the API $export Operation to parse the job exit status and construct links of exported resource type files and response to client.

Initial version of Javabatch Projects for bulk import and export

Missing exception in logs after addHeader, audit, or txn.rollback error

Describe the bug
Under certain circumstances, the server will return a 500 error and there will be no exception details in the server logs.

To Reproduce

1. Implement a fake AuditLogger and configure the FHIR Server to use it.
2. Have it throw an exception when you call the logX methods
3. Issue a request and note the 500 error response
4. Check the logs and note there is no stacktrace

Expected behavior
All 500 errors should result in an exception in the server logs.

Additional context
We always had this issue, but since we weren't doing much of anything in the finally block, we never hit it. We recently moved audit logging to the finally block at the end of the interactions and this has widened

I suggest we move the log statement to the REST interaction methods (create, update, read, etc. instead of the doCreate, doUpdate, doRead variants).

Enhance bulkexport javabatch job to return the number of resources inside each exported ndjson file

"output": [
    {
        "type": "Practitioner",
        "url": "http://serverpath2/practitioner_file_1.ndjson",
        "count": 10000
    },

....

Cleanup fhir-persistence-jdbc tests

We should either revive the tests under com.ibm.watson.health.fhir.persistence.jdbc.search.test or create something comparable.
The idea is to systematically define search parameter definitions for each combination of SearchParameter type and target element type.

Perhaps some of the other tests are worth reviving as well. If not, then they should be deleted.

Acceptance criteria 1: Unit tests (under either fhir-search or fhir-persistence or both) cover search parameters of each search parameter type and each fhir data type.
Acceptance criteria 2: Unit tests that are not executed are deleted (or have a clear comment about why they are still needed but aren't included in the build)

FHIR 4.0.0 Documentation

This epic covers user stories related to documentation of the FHIR server and its components.

FHIR Performance enhancement for R1

This epic covers user stories related to performance of the FHIR server and its components.

Work should be timeboxed and guided by needs of upcoming announcement.
Numbers should be repeatable.

Update the server.xml to reflect the OpenSource pacakage name in the trace specification.

Update the server.xml to reflect the OpenSource pacakage name in the trace specification.

<logging traceSpecification="=info:com.ibm.watsonhealth.fhir.=finer" traceFormat="BASIC"/>

<logging traceSpecification="=info:com.ibm.watson.health.fhir.=finer" traceFormat="BASIC"/>

Bulk Export/Import: $export-status Operation support for Delete

Bulk Export/Import $export-status operation support for Delete
The operation should stop the JavaBatch Job.

Input

• After a JavaBatch job is submitted, there is a response which includes the ID.
• Validate the Tenant Id for the Job
• Call the $export-status operation and validate the tenant

Output
400 - Bad Request
404 - Job Execution not found
403 - forbidden access to job (beyond normal 403)
500 - Internal error

Steps

• Use the Java BatchRuntime to access and stop the Job.

Alternative, URL to stop the above job is:
https://localhost:9443/ibm/api/batch/jobexecutions/1?action=stop

Related to Issue #55

On startup, the userlib is required for derbySproc

On startup, the userlib is required for derbySproc. This hard requirement is no longer valid as the derby-sproc is no longer used in R4.

The derby bootstrap (in FHIR Servlet Context Listener) checks for userlib in the server and stops startup if the bootstrap fails.

Configure server to override "self" URIs with external path

Is your feature request related to a problem? Please describe.
We're running the FHIR Server behind a proxy and that proxy modifies the request URLs.

Request come in to an endpoint like https://[host]/wh-fhir-dev/api/v4 but the server is returning URIs like https://[host]/fhir-server/api/v4/$export-status?job=9.

Is there a way to use the origin request URL in the server URLs returned by the server?

I think it affects at least:

• search result self uri
• Bundle entry fullUrl values
• bulkimportexport polling URLs

Describe the solution you'd like
https://[host]/wh-fhir-dev/api/v4
Either:

• a setting the server will use as the "base" in all self uris; or
• a way to tell the server which HTTP header has the original request URI (so it can use that to construct self uris)

Refactor and cleanup javabatch codes

Bulk should accept _outputFormat requests with encoded "+"

Describe the bug
When _outputFormat is submitted as a query parameter, the UriInfo injected in FHIRResource replaces the "+" char with a space.

This is the same issue we hit with the FHIR "_format" query parameter, but in a different part of the code.

To Reproduce
{{http}}://{{host}}:{{port}}/{{basePath}}/$export?_outputFormat=application/fhir+ndjson&_since=2019-01-01T08:21:26.94-04:00&_type=Patient

Expected behavior
Not sure if its liberty or JAX-RS or CXF at fault here, but we need to work around the issue for this to work.

Refine $import, $export and $export-status operations

Refine $import, $export and $export-status operations

• confirm the multi-tenancy
• resolve TODO
• refactor to support DELETE operations
• push batch code down to the library for bulkdata and pull into the Operation

Reference - https://javaee.github.io/tutorial/batch-processing006.html#BCGCAHCB

 <dependency>
            <groupId>javax.batch</groupId>
            <artifactId>javax.batch-api</artifactId>
            <version>1.0.1</version>
        </dependency>


 JobOperator jobOperator = BatchRuntime.getJobOperator();
        jobOperator.start("FhirBulkExportChunkJob", toProperties(properties));


 private Properties toProperties(Map<String,String> props){
        Properties properties = new Properties();
        for(Entry<String, String> entry : props.entrySet()) {
            properties.put(entry.getKey(), entry.getValue());
        }
        
        return properties;
    }

Add DB2 on Cloud setup/configuration docs

Is your feature request related to a problem? Please describe.
Document the setup and configuration of DB2 on Cloud as a persistence provider for FHIR R4.

Describe the solution you'd like
A markdown document

Describe alternatives you've considered
Is there anything better than markdown?

Additional context
N/A

Custom operation should support more types being passed from URI

Describe the bug
While trying to invoke $export operation via GET, it complains that we can't process an input parameter of type instant.

To Reproduce
Invoke export with a request like this: {{http}}://{{host}}:{{port}}/{{basePath}}/$export?_outputFormat=application/fhir+ndjson&_since=2019-01-01T08:21:26.94-04:00&_type=Patient

Additional context
Spec says we should support passing of "primitive" types via URL.

Refactor FHIRValidator for profile validation with FHIRRegistry

Connectathon Issues with Bulkdata

Connectathon Issues with Bulkdata

Enhance JavaBatch to be able to use one single COS object for exporting.

Implement $apply for PlanDefinition/CarePlan

$apply is a FHIR Operation which captures the current subject, and generates a CarePlan relative to the current subject using the PlanDefinition. $apply is idempotent, and generates the same results over-and-over again based on the subjects data.

URLs
URL: [base]/PlanDefinition/$apply
URL: [base]/PlanDefinition/[id]/$apply

The Operation definition includes many specifics on the $apply function and must be implemented with corresponding tests.

Reference
Plan Definition - http://hl7.org/fhir/plandefinition.html
Operation - http://hl7.org/fhir/plandefinition-operation-apply.html
Connectathon Track - https://confluence.hl7.org/display/FHIR/2019-09+Care+Planning+and+Management+Track

FHIR Profiling

This epic covers user stories related to profiling of the FHIR specification.

Conformance Registry

Create a registry that holds conformance resources (e.g. structure definitions, value sets, etc.) that other components can use for various purposes.

documenation for bulkimport

BulkExport Enhancements

Includes enhancements needed to be compliant with the Spec.

https://build.fhir.org/ig/HL7/bulk-data/export/index.html

Implement $import and $export operations

Implement $import and $export operations so the JavaBatch framework can be added to the operation.

Query Parameters

• _outputFormat
• _since
• _type

Response
In-Progress
Error
Complete

Reference

• https://build.fhir.org/ig/HL7/bulk-data/export/index.html
• https://www.hl7.org/documentcenter/public_temp_45E1557F-1C23-BA17-0CF72AF5739BC769/calendarofevents/himss/2018/HL7%20FHIR%20Bulk%20Data%20API.pdf

Refine and Update the Project POMs for Consistency

fhir-install missing bulkimportexport-webapp yet has specified in assembly.

• add dependency

        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-bulkimportexport-webapp</artifactId>
            <version>${project.version}</version>
            <type>war</type>
        </dependency>

• check to see other dependencies are specified.

fhir-coverage-reports missing code coverage dependencies

• add dependencies

        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-task-api</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-task-core</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-database-utils</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-operation-bulkdata</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-operation-apply</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-bulkimportexport</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-conformance</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-client</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-cli</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>fhir-persistence-schema</artifactId>
            <version>${project.version}</version>
        </dependency>

fhir-task-core reference invalid version

• update 4.0.0 to 4.0.0-SNAPSHOT

    <parent>
        <groupId>com.ibm.watson.health</groupId>
        <artifactId>fhir-parent</artifactId>
        <version>4.0.0</version>
        <relativePath>../fhir-parent</relativePath>
    </parent>

fhir-bulkimportexport update bulkimportexport

• add exclusion for derbytools

        <dependency>
            <groupId>com.ibm.watson.health</groupId>
            <artifactId>fhir-persistence-jdbc</artifactId>
            <version>4.0.0-SNAPSHOT</version>
            <exclusions>
                <exclusion>
                    <groupId>org.apache.derby</groupId>
                    <artifactId>derbytools</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

• put in dependency management

        <dependency>
            <groupId>com.ibm.cos</groupId>
            <artifactId>ibm-cos-java-sdk</artifactId>
            <version>2.1.0</version>
        </dependency>
        <dependency>
            <groupId>javax.batch</groupId>
            <artifactId>javax.batch-api</artifactId>
            <version>1.0</version>
        </dependency>
        <dependency>
            <groupId>javax.inject</groupId>
            <artifactId>javax.inject</artifactId>
            <version>1</version>
        </dependency>

• change inject to

<dependency>
    <groupId>jakarta.inject</groupId>
    <artifactId>jakarta.inject-api</artifactId>
    <version>1.0</version>
</dependency>

• change batch api

<dependency>
    <groupId>jakarta.batch</groupId>
    <artifactId>jakarta.batch-api</artifactId>
    <version>1.0.2</version>
</dependency>

Rough Dependency Hierarchy

Update build for OpenJDK 11

Update build for OpenJDK 11

Remove all references to the "basic" schema

We used to have multiple relational schemas:

1. a "basic" schema that puts all resource types into the same tables
2. a "normalized" schema that uses a set of tables per resource type

At the implementation level, the normalized schema extends the basic schema, which makes things more complicated than they need to be. We never updated the "basic" schema for R4 and so this is needless complexity.

Acceptance criteria 1: Class hierarchy in fhir-persistence-jdbc should be simplified and without reference to the basic schema
Acceptance criteria 2: Configuration and documentation related to the "basic" schema should be removed

Out of Date File in fhir-audit

During a review of the codebase on August 30, 2019, we identified an out-of-date and unused file with key iv used for ondisk encryption of logs. The file is fhir-audit/src/main/resources/config.properties

There are no running instances which use the library that use this configuration file specific to audit.
There is no compilable code which uses the config.properties.

The team has opted to remove the unused file.

DB2 configuration for JavaBatch

For persistence of the javabatch jobs, DB2 will be used per instruction here https://www-01.ibm.com/support/docview.wss?uid=tss1wp102544&aid=11 page 14 and page 17

ValueSet Binding Annotation on Model Classes

Create an @binding annotation on model classes that facilitates conformance validation at runtime.

Saxon TransformerFactory implementation closes XMLStreamWriter in a StAXResult

The fhir-benchmark project brings in Saxon as a dependency which closes the XMLStreamReader when it's finished writing Narrative XHTML content. We need to implement a non-closing XMLStreamWriter delegate to avoid this scenario.

Create Examples of Using Builders

Create Examples of Using Builders

Add field-level comments and invariants to builder setter javadoc

The FHIR definition for each fields consists of:

• Definition
• Binding
• Type
• Comments
• Invariants

Today only the first 3 are apparent from the API. Invariants are captured as annotations on the model classes, but that is hidden during normal usage.

Often times the comments are redundant with the Definition and/or Invariants, but for completeness I think we should be adding all 3 to the corresponding setter methods on the Builders.

Multiple-Nodes javabatch deployment

During Connectathon, we found the job submission was very slow, from the logs, looks like the job submission response was only returned after the job was actually finished. We hope separating job dispatch and executor can make the job submission faster.