IBM FHIR Server 4.6.1

This version of the IBM FHIR Server supports HL7 FHIR Specification version v4.0.1.

This release focuses on fixing bulk import/export bugs, adding additional search options, and introduces an initial implementation of the Patient/$everything operation.

Added

• VERSION to the xx_LOGICAL_RESOURCES
  • this sets us up to reduce the number of joins in select queries (#1385)
  • see migration considerations
• $everything operation
  • note that this operation is not yet included in the default fhir server installer / docker image; add the jar to the server's userlib directory to enable it
• Support _total parameter in search requests
• Support for searching references by identifier
  • requires reindex, per migration considerations
• Support token modifier ':of-type'
  • requires reindex, per migration considerations

Changed

• Make useStoredCompartmentParam the default
  • when migrating from versions prior to 4.5.1, a reindex will be required for proper compartment search behavior (unless useStoredCompartmentParam is explicitly set to false)
  • see migration considerations for additional reindex information
• File-based export should start writing earlier
• File-based exports should be organized by subdirectory
• Replace ByteArrayInputStream and ByteArrayOutputStream usage with more efficient solution
• Use the internal patient compartment search parameter during Patient/Group export

Fixed

• Reindex on Db2 doesn't execute with MT_ID flag
• fhir-persistence-schema doesn't drop schemas as expected on postgres
• Under certain conditions, $reindex attempts to index a deleted resource
• Under certain conditions, bulk import fails to acquire a db connection
• Patient Export without Type results in a failed export
• References in Patient Export are not honored
• Patient Export Results in duplicate data included in the Write.
• Patient resources are is not exported when asked for during Group Export
• File-based export writes empty files
• $import is skipping the first entry in the import file
• Overall total and importRate metrics are wrong after bulk data import

Security

• Relative path enables malicious content to be imported or /dev/null

Migration Considerations

To migrate from a prior version of the IBM FHIR Server to version 4.6.1:

1. Analyze configuration changes and prepare for the upgrade
   • See #2111 for a change in the default value of fhirServer/search/useStoredCompartmentParam
2. Stop the server (or otherwise prevent write requests).
3. Perform a database back up.
4. Run the fhir-persistence-schema-4.6.1-cli.jar --update-schema command. If using a non-admin user (recommended), also perform the --grant-to action. Note: it is no longer necessary to separately invoke --refresh-tenants.
5. Deploy the new server.
6. Perform re-indexing.
   • Needed for #773 and #1323

Special considerations for upgrading to 4.6.1:

• For #2109 we added a column to the xx_LOGICAL_RESOURCES tables. The --update-schema action will automatically fill in the data, but the execution time will be dependent on the number of resources to backfill.

Using the Release

Run or extend the Docker image from https://hub.docker.com/r/ibmcom/ibm-fhir-server or download fhir-server-distribution.zip and install as described at https://ibm.github.io/FHIR/guides/FHIRServerUsersGuide.

Executable jar files for the fhir-persistence-schema, fhir-swagger-generator, and fhir-bucket projects are also available:

• fhir-persistence-schema-4.6.1-cli.jar
• fhir-swagger-generator-4.6.1-cli.jar
• fhir-bucket-4.6.1-cli.jar

Usage is documented in the corresponding README files:

• https://github.com/IBM/FHIR/tree/master/fhir-persistence-schema
• https://github.com/IBM/FHIR/tree/master/fhir-swagger-generator
• https://github.com/IBM/FHIR/tree/master/fhir-bucket

For Maven users, all project binaries are posted to BinTray with a version of 4.6.1.