Change Docker Compose

Fixes: #184

Also updated README

README.md

@@ -34,28 +34,30 @@ docker run -p 8080:8080 ghcr.io/medizininformatik-initiative/flare:2.3
 
 ## Environment Variables
 
-| Name | Default | 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][1]. |
-| FLARE_CACHE_MEM_REFRESH | PT24H | The duration after which in-memory cache entries should be refreshed in [ISO 8601 durations][1]. |
-| 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][1]. |
-| 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 | The mappings to use. |
-| FLARE_MAPPING_CONCEPT_TREE_FILE | ontology/codex-code-tree.json | The code tree to use. |
-| 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 |
+| 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][1]. |
+| FLARE_CACHE_MEM_REFRESH | PT24H | | The duration after which in-memory cache entries should be refreshed in [ISO 8601 durations][1]. |
+| 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][1]. |
+| 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. |
+| 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
 

docker-compose.yml

@@ -1,13 +1,31 @@
 services:
- data-store:
- image: "samply/blaze:0.29"
- environment:
- BASE_URL: "http://localhost:8082"
- JAVA_TOOL_OPTIONS: "-Xmx1g"
- LOG_LEVEL: "debug"
+ flare:
+ image: ghcr.io/medizininformatik-initiative/flare:2.3.0
  ports:
- - "8082:8080"
+ - 8080:8080
+ environment:
+ FLARE_FHIR_SERVER: ${FLARE_FHIR_SERVER_URL:-http://fhir-server:8080/fhir/}
+ FLARE_FHIR_USER: ${FLARE_FHIR_USER:-}
+ FLARE_FHIR_PASSWORD: ${FLARE_FHIR_PW:-}
+ FLARE_FHIR_OAUTH_ISSUER_URI: ${FLARE_FHIR_OAUTH_ISSUER_URI}
+ FLARE_FHIR_OAUTH_CLIENT_ID: ${FLARE_FHIR_OAUTH_CLIENT_ID}
+ FLARE_FHIR_OAUTH_CLIENT_SECRET: ${FLARE_FHIR_OAUTH_CLIENT_SECRET}
+ FLARE_FHIR_MAX_CONNECTIONS: ${FLARE_FHIR_MAX_CONNECTIONS:-32}
+ FLARE_FHIR_MAX_QUEUE_SIZE: ${FLARE_FHIR_MAX_QUEUE_SIZE:-500}
+ FLARE_FHIR_PAGE_COUNT: ${FLARE_FHIR_PAGE_COUNT:-500}
+ FLARE_CACHE_MEM_SIZE_MB: ${FLARE_CACHE_MEM_SIZE_MB:-1024}
+ FLARE_CACHE_MEM_EXPIRE: ${FLARE_CACHE_MEM_EXPIRE:-PT48H}
+ FLARE_CACHE_MEM_REFRESH: ${FLARE_CACHE_MEM_REFRESH:-PT24H}
+ FLARE_CACHE_DISK_PATH: ${FLARE_CACHE_DISK_PATH:-cache}
+ FLARE_CACHE_DISK_EXPIRE: ${FLARE_CACHE_DISK_EXPIRE:-P7D}
+ FLARE_CACHE_DISK_THREADS: ${FLARE_CACHE_DISK_THREADS:-4}
+ JAVA_TOOL_OPTIONS: ${FLARE_JAVA_TOOL_OPTIONS:--Xmx4g}
+ LOG_LEVEL: ${FLARE_LOG_LEVEL:-info}
  volumes:
- - "data-store-data:/app/data"
+ - type: volume
+ source: flare-cache
+ target: /app/cache
+
 volumes:
- data-store-data:
+ flare-cache:
+ name: "flare-cache"