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FLARE

Feasibility Analysis Request Executor

Goal

The goal of this project is to provide a service that allows for execution of feasibility queries on a FHIR-server.

Build

mvn clean install

Run

docker-compose up

In order for flare to work, a FHIR server such as Blaze must be running on port 8082 by default.

Environment Variables

Name Default Depr ¹ Description
FLARE_FHIR_SERVER http://localhost:8082/fhir The base URL of the FHIR server to use.
FLARE_FHIR_USER The username to use for HTTP Basic Authentication.
FLARE_FHIR_PASSWORD The password to use for HTTP Basic Authentication.
FLARE_FHIR_OAUTH_ISSUER_URI The issuer URI of the OpenID Connect provider.
FLARE_FHIR_OAUTH_CLIENT_ID The client ID to use for authentication with OpenID Connect provider.
FLARE_FHIR_OAUTH_CLIENT_SECRET The client secret to use for authentication with OpenID Connect provider.
FLARE_FHIR_MAX_CONNECTIONS 4 The maximum number of connections Flare opens towards the FHIR server.
FLARE_FHIR_MAX_QUEUE_SIZE 500 The maximum number FHIR server requests Flare queues before returning an error.
FLARE_FHIR_PAGE_COUNT 1000 The number of resources per page to request from the FHIR server.
FLARE_CACHE_MEM_SIZE_MB 1024 The size of the in-memory cache in mebibytes.
FLARE_CACHE_MEM_EXPIRE PT48H The duration after which in-memory cache entries should expire in ISO 8601 durations.
FLARE_CACHE_MEM_REFRESH PT24H The duration after which in-memory cache entries should be refreshed in ISO 8601 durations.
FLARE_CACHE_DISK_PATH cache The name of the directory in which the on-disk cache should be written.
FLARE_CACHE_DISK_EXPIRE P7D The duration after which on-disk cache entries should expire in ISO 8601 durations.
FLARE_CACHE_DISK_THREADS 4 The number of threads the disk cache should use for reading and writing entries.
FLARE_MAPPING_MAPPING_FILE ontology/codex-term-code-mapping.json v2.4.0 The mappings to use.
FLARE_MAPPING_CONCEPT_TREE_FILE ontology/codex-code-tree.json v2.4.0 The code tree to use.
FLARE_ENABLE_COHORT_ENDPOINT false Set to true to enable the cohort extraction endpoint, which returns the actual patient IDs.
SERVER_PORT 8080 The port at which Flare provides its REST API.
JAVA_TOOL_OPTIONS -Xmx4g JVM options (Docker only)
LOG_LEVEL info one of trace, debug, info, warn or error

¹ Deprecated since

Default Configuration

The default configuration assumes the following:

  • there is about 8 GiB of memory available for Flare
    • 4 GiB JVM heap including 1 GiB in-memory Cache
    • about 1 GiB JVM off-heap memory especially for the disk-based cache
    • about 3 GiB for page cache and the rest of the operating system
  • there is plenty of disk space
    • the disk space used by the disk-based cache is not constrained right now
    • cache entries life for at least 7 days per default
    • disk space is only reclaimed on a best-effort base
  • the FHIR endpoint is capable of handling 4 requests in parallel
  • the FHIR endpoint is capable of returning pages of size 1000 or constrain the page size itself

Support for self-signed certificates

Flare supports the use of self-signed certificates from your own CAs. On each startup FLARE will search through the folder /app/certs inside the container , add all found CA *.pem files to a java truststore and start FLARE with this truststore.

In order to add your own CA files, add your own CA *.pem files to the /app/certs folder of the container.

Using docker-compose mount a folder from your host (e.g.: ./certs) to the /app/certs folder, add your *.pem files (one for each CA you would like to support) to the folder and ensure that they have the .pem extension.

Documentation

FHIR Endpoint Requirements

The FHIR endpoint used by FLARE (see FLARE_FHIR_SERVER) has to support the following parts of the FHIR specification:

  • the search result parameters _count and _elements should be supported for optimal performance

License

Copyright ???

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.