From facb3fab087fc41206cde306529f87ba5496c37f Mon Sep 17 00:00:00 2001 From: saolberg Date: Tue, 25 May 2021 23:26:28 -0300 Subject: [PATCH 1/5] postgres included --- docker-compose.yml | 19 ++++++++++--------- pom.xml | 2 +- src/main/resources/application.yaml | 23 +++++++++++------------ 3 files changed, 22 insertions(+), 22 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index cd25605..2453220 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,16 +6,17 @@ services: restart: on-failure ports: - "8080:8080" - hapi-fhir-mysql: - image: mysql:latest - container_name: hapi-fhir-mysql + db: + image: postgres:latest + container_name: postgres restart: always environment: - MYSQL_DATABASE: 'hapi' - MYSQL_USER: 'admin' - MYSQL_PASSWORD: 'admin' - MYSQL_ROOT_PASSWORD: 'admin' + POSTGRES_PASSWORD: 'admin' + POSTGRES_USER: 'admin' + POSTGRES_DB: 'fhir' + ports: + - 5000:5432 volumes: - - hapi-fhir-mysql:/var/lib/mysql + - fhirData:/var/lib/postgresql/data volumes: - hapi-fhir-mysql: \ No newline at end of file + fhirData: diff --git a/pom.xml b/pom.xml index 4471c2f..2cf540c 100644 --- a/pom.xml +++ b/pom.xml @@ -62,7 +62,7 @@ org.postgresql postgresql - 42.2.9 + 42.2.20 diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml index ea9bfa3..5a014ec 100644 --- a/src/main/resources/application.yaml +++ b/src/main/resources/application.yaml @@ -1,10 +1,9 @@ spring: datasource: - url: 'jdbc:h2:file:./target/database/h2' - #url: jdbc:h2:mem:test_mem - username: sa - password: null - driverClassName: org.h2.Driver + url: 'jdbc:postgresql://db:5432/fhir' + username: admin + password: admin + driverClassName: org.postgresql.Driver max-active: 15 # database connection pool size @@ -14,7 +13,7 @@ spring: properties: hibernate.format_sql: false hibernate.show_sql: false -# hibernate.dialect: org.hibernate.dialect.h2dialect + hibernate.dialect: org.hibernate.dialect.PostgreSQL95Dialect # hibernate.hbm2ddl.auto: update # hibernate.jdbc.batch_size: 20 # hibernate.cache.use_query_cache: false @@ -22,12 +21,12 @@ spring: # hibernate.cache.use_structured_entries: false # hibernate.cache.use_minimal_puts: false ### These settings will enable fulltext search with lucene -# hibernate.search.enabled: true -# hibernate.search.backend.type: lucene -# hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer -# hibernate.search.backend.directory.type: local-filesystem -# hibernate.search.backend.directory.root: target/lucenefiles -# hibernate.search.backend.lucene_version: lucene_current + hibernate.search.enabled: true + hibernate.search.backend.type: lucene + hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer + hibernate.search.backend.directory.type: local-filesystem + hibernate.search.backend.directory.root: target/lucenefiles + hibernate.search.backend.lucene_version: lucene_current batch: job: enabled: false From d06c727984f83bf78571e76edece822eff635875 Mon Sep 17 00:00:00 2001 From: saolberg Date: Wed, 26 May 2021 22:57:38 -0300 Subject: [PATCH 2/5] cache time removed --- es/docker-compose.yml | 26 ++++++++++++++++++++++++++ src/main/resources/application.yaml | 26 +++++++++++++------------- 2 files changed, 39 insertions(+), 13 deletions(-) create mode 100644 es/docker-compose.yml diff --git a/es/docker-compose.yml b/es/docker-compose.yml new file mode 100644 index 0000000..21e2f16 --- /dev/null +++ b/es/docker-compose.yml @@ -0,0 +1,26 @@ +version: "3.0" +services: + elasticsearch: + container_name: es-container + image: docker.elastic.co/elasticsearch/elasticsearch:7.11.0 + environment: + - xpack.security.enabled=false + - "discovery.type=single-node" + networks: + - es-net + ports: + - 9200:9200 + kibana: + container_name: kb-container + image: docker.elastic.co/kibana/kibana:7.11.0 + environment: + - ELASTICSEARCH_HOSTS=http://es-container:9200 + networks: + - es-net + depends_on: + - elasticsearch + ports: + - 5601:5601 +networks: + es-net: + driver: bridge \ No newline at end of file diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml index 5a014ec..d87c2cf 100644 --- a/src/main/resources/application.yaml +++ b/src/main/resources/application.yaml @@ -94,19 +94,19 @@ hapi: search-coord-max-pool-size: 100 search-coord-queue-capacity: 200 -# logger: -# error_format: 'ERROR - ${requestVerb} ${requestUrl}' -# format: >- -# Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] -# Operation[${operationType} ${operationName} ${idOrResourceName}] -# UA[${requestHeader.user-agent}] Params[${requestParameters}] -# ResponseEncoding[${responseEncodingNoDefault}] -# log_exceptions: true -# name: fhirtest.access -# max_binary_size: 104857600 -# max_page_size: 200 -# retain_cached_searches_mins: 60 -# reuse_cached_search_results_millis: 60000 + logger: + error_format: 'ERROR - ${requestVerb} ${requestUrl}' + format: >- + Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] + Operation[${operationType} ${operationName} ${idOrResourceName}] + UA[${requestHeader.user-agent}] Params[${requestParameters}] + ResponseEncoding[${responseEncodingNoDefault}] + log_exceptions: true + name: fhirtest.access + max_binary_size: 104857600 + max_page_size: 200 + retain_cached_searches_mins: 60 + reuse_cached_search_results_millis: 30000 tester: home: name: Local Tester From f44a6feb4448155cc0a9d5b34775674624421384 Mon Sep 17 00:00:00 2001 From: saolberg Date: Thu, 27 May 2021 16:14:03 -0300 Subject: [PATCH 3/5] default schema --- docker-compose.yml | 19 ++++++----- es/docker-compose.yml | 26 --------------- pom.xml | 2 +- src/main/resources/application.yaml | 49 +++++++++++++++-------------- 4 files changed, 35 insertions(+), 61 deletions(-) delete mode 100644 es/docker-compose.yml diff --git a/docker-compose.yml b/docker-compose.yml index 2453220..a53141d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,17 +6,16 @@ services: restart: on-failure ports: - "8080:8080" - db: - image: postgres:latest - container_name: postgres + hapi-fhir-mysql: + image: mysql:latest + container_name: hapi-fhir-mysql restart: always environment: - POSTGRES_PASSWORD: 'admin' - POSTGRES_USER: 'admin' - POSTGRES_DB: 'fhir' - ports: - - 5000:5432 + MYSQL_DATABASE: 'hapi' + MYSQL_USER: 'admin' + MYSQL_PASSWORD: 'admin' + MYSQL_ROOT_PASSWORD: 'admin' volumes: - - fhirData:/var/lib/postgresql/data + - hapi-fhir-mysql:/var/lib/mysql volumes: - fhirData: + hapi-fhir-mysql: diff --git a/es/docker-compose.yml b/es/docker-compose.yml deleted file mode 100644 index 21e2f16..0000000 --- a/es/docker-compose.yml +++ /dev/null @@ -1,26 +0,0 @@ -version: "3.0" -services: - elasticsearch: - container_name: es-container - image: docker.elastic.co/elasticsearch/elasticsearch:7.11.0 - environment: - - xpack.security.enabled=false - - "discovery.type=single-node" - networks: - - es-net - ports: - - 9200:9200 - kibana: - container_name: kb-container - image: docker.elastic.co/kibana/kibana:7.11.0 - environment: - - ELASTICSEARCH_HOSTS=http://es-container:9200 - networks: - - es-net - depends_on: - - elasticsearch - ports: - - 5601:5601 -networks: - es-net: - driver: bridge \ No newline at end of file diff --git a/pom.xml b/pom.xml index 2cf540c..4471c2f 100644 --- a/pom.xml +++ b/pom.xml @@ -62,7 +62,7 @@ org.postgresql postgresql - 42.2.20 + 42.2.9 diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml index d87c2cf..ea9bfa3 100644 --- a/src/main/resources/application.yaml +++ b/src/main/resources/application.yaml @@ -1,9 +1,10 @@ spring: datasource: - url: 'jdbc:postgresql://db:5432/fhir' - username: admin - password: admin - driverClassName: org.postgresql.Driver + url: 'jdbc:h2:file:./target/database/h2' + #url: jdbc:h2:mem:test_mem + username: sa + password: null + driverClassName: org.h2.Driver max-active: 15 # database connection pool size @@ -13,7 +14,7 @@ spring: properties: hibernate.format_sql: false hibernate.show_sql: false - hibernate.dialect: org.hibernate.dialect.PostgreSQL95Dialect +# hibernate.dialect: org.hibernate.dialect.h2dialect # hibernate.hbm2ddl.auto: update # hibernate.jdbc.batch_size: 20 # hibernate.cache.use_query_cache: false @@ -21,12 +22,12 @@ spring: # hibernate.cache.use_structured_entries: false # hibernate.cache.use_minimal_puts: false ### These settings will enable fulltext search with lucene - hibernate.search.enabled: true - hibernate.search.backend.type: lucene - hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer - hibernate.search.backend.directory.type: local-filesystem - hibernate.search.backend.directory.root: target/lucenefiles - hibernate.search.backend.lucene_version: lucene_current +# hibernate.search.enabled: true +# hibernate.search.backend.type: lucene +# hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer +# hibernate.search.backend.directory.type: local-filesystem +# hibernate.search.backend.directory.root: target/lucenefiles +# hibernate.search.backend.lucene_version: lucene_current batch: job: enabled: false @@ -94,19 +95,19 @@ hapi: search-coord-max-pool-size: 100 search-coord-queue-capacity: 200 - logger: - error_format: 'ERROR - ${requestVerb} ${requestUrl}' - format: >- - Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] - Operation[${operationType} ${operationName} ${idOrResourceName}] - UA[${requestHeader.user-agent}] Params[${requestParameters}] - ResponseEncoding[${responseEncodingNoDefault}] - log_exceptions: true - name: fhirtest.access - max_binary_size: 104857600 - max_page_size: 200 - retain_cached_searches_mins: 60 - reuse_cached_search_results_millis: 30000 +# logger: +# error_format: 'ERROR - ${requestVerb} ${requestUrl}' +# format: >- +# Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] +# Operation[${operationType} ${operationName} ${idOrResourceName}] +# UA[${requestHeader.user-agent}] Params[${requestParameters}] +# ResponseEncoding[${responseEncodingNoDefault}] +# log_exceptions: true +# name: fhirtest.access +# max_binary_size: 104857600 +# max_page_size: 200 +# retain_cached_searches_mins: 60 +# reuse_cached_search_results_millis: 60000 tester: home: name: Local Tester From 36916b71ad1e177bdd4372953f9f0b45aa6e22ac Mon Sep 17 00:00:00 2001 From: saolberg Date: Thu, 27 May 2021 16:24:19 -0300 Subject: [PATCH 4/5] cached time readme --- README.md | 5 +++++ docker-compose.yml | 1 + 2 files changed, 6 insertions(+) diff --git a/README.md b/README.md index 5572ac6..4c6af22 100644 --- a/README.md +++ b/README.md @@ -351,6 +351,11 @@ elasticsearch.schema_management_strategy=CREATE Set `hapi.fhir.lastn_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable the $lastn operation on this server. Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch. +## Changing cached search results time + +It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml] is 6000 miliseconds by default. +Set `reuse_cached_search_results_millis: -1` in the [application.yaml] file to ignore the cache time every search. + ## Build the distroless variant of the image (for lower footprint and improved security) The default Dockerfile contains a `release-distroless` stage to build a variant of the image diff --git a/docker-compose.yml b/docker-compose.yml index a53141d..c4ed2cf 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -19,3 +19,4 @@ services: - hapi-fhir-mysql:/var/lib/mysql volumes: hapi-fhir-mysql: + From aa5297d1317d2b59951388ea118a243c52d3ffe6 Mon Sep 17 00:00:00 2001 From: Patrick Werner Date: Tue, 8 Jun 2021 12:56:59 +0200 Subject: [PATCH 5/5] removed empty line --- docker-compose.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index c4ed2cf..a53141d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -19,4 +19,3 @@ services: - hapi-fhir-mysql:/var/lib/mysql volumes: hapi-fhir-mysql: -