release 1.9.0

ahdis · Mar 10, 2022 · 128c395 · 128c395
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commit 128c395
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diff --git a/README.md b/README.md
@@ -12,8 +12,6 @@ a public test server is hosted at [https://test.ahdis.ch/matchbox/fhir](https://
 ## containers
 
 The docker file will create a docker image with no preloaded implementation guides. A list of implementation guides to load can be passed as config-map.
-A second docker file will create an image with fixed configuration and preloaded implementation guides.  That docker image does not need to download the implementation guides afterwards.
-
 ## Prerequisites
 
 - [This project](https://github.com/ahdis/matchbox) checked out. You may wish to create a GitHub Fork of the project and check that out instead so that you can customize the project and save the results to GitHub. Check out the main branch (master is kept in sync with [hapi-fhir-jpaserver-starter](https://github.com/hapifhir/hapi-fhir-jpaserver-starter)
@@ -30,7 +28,7 @@ With no implementation guide:
 ```bash
 mvn clean install -DskipTests spring-boot:run
 ```
-Load example implementation guides:
+Load example implementation guides (needs postgres):
 ```bash
 mvn clean install -DskipTests spring-boot:run -Dspring-boot.run.arguments=--spring.config.additional-location=file:with-preload/application.yaml
 ```
@@ -47,10 +45,21 @@ mvn clean install -DskipTests spring-boot:run -Dspring-boot.run.jvmArguments="-X
 Then, browse to the following link to use the server:
 
 [http://localhost:8080/matchbox/fhir](http://localhost:8080/matchbox/fhir)
+or
+[http://localhost:8080/matchbox/#/](http://localhost:8080/matchbox/#/)
 
 ## Using docker-compose with a persistent postgreSQL database
 
-The database will be stored in the "data" directory. The configuration can be found in the "with-postgres" directory.
+The database will be stored in the "data" directory. The configuration can be found in the "with-postgres" directory or in the "with-preload" directory.
+
+Change to either with-posgres directory or the with-preload directory (contains a list of swiss ig's).
+
+For the first time, you might need to do 
+
+```
+docker-compose up matchbox-db
+```
+that the database gets initialized before matchbox is starting up (needs a fix)
 
 ```
 mkdir data
@@ -60,7 +69,7 @@ docker-compose up
 ```
 
 matchbox will be available at [http://localhost:8080/matchbox/fhir](http://localhost:8080/matchbox/fhir)
-matchbox-formfiller will be available at [http://localhost:4300/matchbox-formfiller/#/](http://localhost:4300/matchbox-formfiller/#/)
+matchbox-gui will be available at [http://localhost:8080/matchbox/#/](http://localhost:8080/matchbox/#/)
 
 
 Export the DB data:
@@ -88,21 +97,11 @@ Server will then be accessible at http://localhost:8080/matchbox/fhir/metadata.
 To dynamically configure run in a kubernetes environment and add a kubernetes config map that provides /config/application.yaml file with implementation guide list like in "with-preload/application.yaml" 
 
 
-### Image with preloaded implementation guides
-
-After building the base image:
-```bash
-cd with-preload
-docker build -t matchbox-swissepr .
-docker run -d --name matchbox-swissepr -p 8080:8080 matchbox-swissepr
-```
-
 ### making container available
 ```
-docker tag matchbox eu.gcr.io/fhir-ch/matchbox:v182
+docker tag matchbox eu.gcr.io/fhir-ch/matchbox:v190
 
-docker push eu.gcr.io/fhir-ch/matchbox:v182
-docker push eu.gcr.io/fhir-ch/matchbox-swissepr:v170
+docker push eu.gcr.io/fhir-ch/matchbox:v190
 ```
 
 API

diff --git a/changelog.md b/changelog.md
@@ -1,6 +1,8 @@
-2022/03/09 Release 1.9.0
+2022/03/10 Release 1.9.0
 - Updated to hap-fhir 5.7.0, fhir.core.version (validator) 5.6.27
 - Extended Mobile Access Gateway support for PMP (replacing FHIR documents with selected Patient in Mobile Access Gateway, transforming to CDA and MDH publish)
+- base release with no ig's configured: docker pull eu.gcr.io/fhir-ch/matchbox:v190
+- docker-compose setup for postgres and for postgres and swiss igs
 
 2022/02/21 Release 1.8.2
 - OAuth integration for [Mobile Access Gateway](https://github.com/i4mi/MobileAccessGateway) in webapp

diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java b/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
@@ -368,10 +368,10 @@ protected void initialize() throws ServletException {
 
     // If subscriptions are enabled, we want to register the interceptor that
     // will activate them and match results against them
-    if (appProperties.getSubscription() != null) {
+    // FIXME not specified but is still triggered: if (appProperties.getSubscription() != null) {
       // Subscription debug logging
-      interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
-    }
+      // interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
+    // }
 
     // Cascading deletes
 

diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml
@@ -20,7 +20,7 @@ spring:
     properties:
       hibernate.format_sql: false
       hibernate.show_sql: false
-  #      hibernate.dialect: org.hibernate.dialect.h2dialect
+      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
   #      hibernate.hbm2ddl.auto: update
   #      hibernate.jdbc.batch_size: 20
   #      hibernate.cache.use_query_cache: false

diff --git a/docker-compose.yml → with-postgres/docker-compose.yml b/docker-compose.yml → with-postgres/docker-compose.yml
diff --git a/with-preload/Dockerfile b/with-preload/Dockerfile
diff --git a/with-preload/application.yaml b/with-preload/application.yaml
@@ -1,3 +1,19 @@
+server:
+  servlet:
+    context-path: /matchbox
+spring:
+  datasource:
+    url: 'jdbc:postgresql://matchbox-db:5432/matchbox'
+    username: matchbox
+    password: matchbox
+    driverClassName: org.postgresql.Driver
+
+    # database connection pool size
+    hikari:
+      maximum-pool-size: 10
+  jpa:
+    properties:
+      hibernate.dialect: org.hibernate.dialect.PostgreSQL95Dialect
 hapi:
   fhir:
     implementationguides:
@@ -8,26 +24,22 @@ hapi:
       cdach:
         url: http://build.fhir.org/ig/hl7ch/cda-fhir-maps/package.tgz
         name: ch.fhir.ig.cda-fhir-maps
-        version: 0.2.0
+        version: 0.3.0
       iheformatcodefhir:
-        url: https://profiles.ihe.net/fhir/ihe.formatcode.fhir/package.tgz
         name: ihe.formatcode.fhir
         version: 1.0.0
-#      terminology:
-#       name: hl7.terminology.r4
-#       version: 2.1.0
       eprterm:
         name: ch.fhir.ig.ch-epr-term
-        version: 2.0.6
+        version: 2.0.7
       core:
         name: ch.fhir.ig.ch-core
         version: 2.0.0
       emed:
         name: ch.fhir.ig.ch-emed
-        version: 1.0.0
+        version: 2.0.0
       vacd:
         name: ch.fhir.ig.ch-vacd
-        version: 1.0.0
+        version: 2.0.0
       atc:
         name: ch.fhir.ig.ch-atc
         version: 3.1.0
@@ -36,31 +48,26 @@ hapi:
         version: 2.7.0
       chorf:
         name: ch.fhir.ig.ch-orf
-        version: 0.10.0
+        version: 1.0.0
       chradorder:
         name: ch.fhir.ig.ch-rad-order
-        version: 0.1.0
+        version: 1.0.0
+      hl7fhiruvips:
+        name: hl7.fhir.uv.ips
+        version": 1.0.0
       chetoc:
         name: ch.fhir.ig.ch-etoc
-        version: 0.1.0
+        version: 1.0.0
+        url: https://build.fhir.org/ig/hl7ch/ch-etoc/branches/main/package.tgz
       mhd:
         name: ihe.mhd.fhir
-        version: 4.0.1      
+        version: 4.0.1
       pixm:
         name: IHE.ITI.PIXm
         version: 3.0.0
       cheprmhealth:
-        url: https://fhir.ch/ig/ch-epr-mhealth/package.tgz
         name: ch.fhir.ig.ch-epr-mhealth
         version: 1.0.0
       challergyintolerance:
         name: ch.fhir.ig.ch-allergyintolerance
-        version": 0.2.0
-      chradorderpoc:
-        url: https://build.fhir.org/ig/ahdis/ch-rad-poc/package.tgz
-        name: ch.ahdis.ig.ch-rad-poc
-        version: 0.1.0
-      chalis:
-        url: https://build.fhir.org/ig/ahdis/ch-alis/package.tgz
-        name: ch.fhir.ig.ch-alis
-        version": 0.2.0
+        version": 1.0.0
diff --git a/with-preload/docker-compose.yml b/with-preload/docker-compose.yml
@@ -0,0 +1,27 @@
+services:
+  matchbox:
+    # build: .
+    image: matchbox:latest
+    container_name: matchbox
+    restart: on-failure
+    ports:
+      - "8080:8080"
+    links:
+      - matchbox-db
+    volumes:
+      - ./with-preload:/config      
+  matchbox-db:
+    image: postgres:latest
+    container_name: matchbox-db
+    restart: always
+    # Comment out to not log queries
+    command: ["postgres", "-c", "log_statement=all"]
+    # End comment out
+    ports:
+      - "5432:5432"
+    environment:
+      POSTGRES_DB: 'matchbox'
+      POSTGRES_USER: 'matchbox'
+      POSTGRES_PASSWORD: 'matchbox'     
+    volumes:
+      - ./data:/var/lib/postgresql/data