Add Docu

.dockerignore

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+*
+!fhir
+!src
+!Dockerfile
+!project.clj

Dockerfile

@@ -1,7 +1,14 @@
+FROM clojure:lein-2.8.1 as build
+
+COPY . /build/
+
+WORKDIR /build
+RUN lein uberjar
+
 FROM openjdk:8u191-jre-alpine3.9
 
-COPY target/life-fhir-store-0.1-SNAPSHOT-standalone.jar /app/
-COPY fhir /app/
+COPY --from=build /build/target/life-fhir-store-0.1-SNAPSHOT-standalone.jar /app/
+COPY fhir /app/fhir/
 
 WORKDIR /app
 

README.md

@@ -1,14 +1,82 @@
-# Life FHIR Store
+# LIFE FHIR Store
 
 A FHIR Store including a CQL Engine based on Datomic.
 
 ## Usage
 
-FIXME
+You need Docker to run the LIFE FHIR Store. The most convenient way is to check out this repository and use the `docker-compose.yml` to bring the LIFE FHIR Store up. The default memory requirements are 4 GB. You also need to have port 8080 free on your host.
+
+To start the LIFE FHIR Store, type:
+
+```bash
+docker-compose up
+```
+
+You should see a output similar to:
+
+```
+Creating volume "life-fhir-store_db-data" with default driver
+Recreating life-fhir-store_db_1 ... done
+Recreating life-fhir-store_store_1 ... done
+Attaching to life-fhir-store_db_1, life-fhir-store_store_1
+db_1     | Launching with Java options -server -Xms1g -Xmx1g -XX:+UseG1GC -XX:MaxGCPauseMillis=50
+db_1     | Starting datomic:free://0.0.0.0:4334/<DB-NAME>, storing data in: /data ...
+db_1     | System started datomic:free://0.0.0.0:4334/<DB-NAME>, storing data in: /data
+store_1  | 19-03-29 08:57:48 52816fd744d6 INFO [life-fhir-store.system:110] - Read structure definitions from: /app/fhir/r4 resulting in: Address, Annotation, Period, CodeableConcept, Organization, Encounter, Specimen, Bundle, Coding, Patient, Range, ContactPoint, Meta, Quantity, HumanName, DeviceMetric, SampledData, Ratio, Device, Reference, Identifier, Narrative, Observation
+store_1  | 19-03-29 09:13:09 bc25669b9f17 INFO [life-fhir-store.system:90] - Created database at: datomic:free://db:4334/dev
+store_1  | 19-03-29 09:13:09 bc25669b9f17 INFO [life-fhir-store.system:93] - Connect with database: datomic:free://db:4334/dev
+store_1  | 19-03-29 09:13:10 bc25669b9f17 INFO [life-fhir-store.system:98] - Upsert schema in database: datomic:free://db:4334/dev creating 2300 new facts
+store_1  | 19-03-29 09:13:10 bc25669b9f17 INFO [life-fhir-store.server:33] - Start server on port 8080
+store_1  | 19-03-29 09:13:10 bc25669b9f17 INFO [life-fhir-store.core:49] - Maximum available memory: 2048
+store_1  | 19-03-29 09:13:10 bc25669b9f17 INFO [life-fhir-store.core:50] - Number of available processors: 4
+```
+
+In order to test connectivity, you can query the health endpoint:
+
+```bash
+curl http://localhost:8080/health
+```
+
+It should return `OK`.
+
+### Upload FHIR Resources
+
+before you can issue CQL queries against the LIFE FHIR Store, you have to upload some FHIR resources. If you have none, you can generate them y using the [FHIR Test Data Generator][1].
+
+```bash
+life-fhir-gen -n1 > bundle.json
+```
+
+Next you need to upload that `bundle.json` to the LIFE FHIR Store:
+
+```bash
+curl -d @bundle.json http://localhost:8080/fhir
+```
+
+The result should be:
+
+```
+{"message":"OK","t":<some number>}
+```
+
+### Issuing a CQL Query
+
+The most convenient way is to use the [CQL Runner][2]. You have to go into the `Config` menu and set the `CQL Engine` to `http://localhost:8080/cql/evaluate`. The other config options doesn't matter because the CQL Engine of the LIFE FHIR Store always uses its own internal data.
+
+### Deleting the Data Volume
+
+If you like to restart with a fresh database, you have to delete the data volume. You can do this by typing:
+
+```bash
+docker volume rm life-fhir-store_db-data
+```
 
 ## License
 
 Copyright © 2019 LIFE Research Center (Alexander Kiel)
 
 Distributed under the Eclipse Public License either version 1.0 or (at
 your option) any later version.
+
+[1]: <https://github.com/life-research/life-fhir-gen>
+[2]: <http://cql-runner.dataphoria.org/>

docker-compose.yml

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+version: '3.2'
+services:
+  db:
+    image: "akiel/datomic-free:0.9.5656"
+    environment:
+      ALT_HOST: db
+    volumes:
+    - "db-data:/data"
+  store:
+    image: "f471ce7b017d"
+    environment:
+      DATABASE_URI: "datomic:free://db:4334/dev"
+      STRUCTURE_DEFINITIONS_PATH: "/app/fhir/r4"
+      JVM_OPTS: "-server -Xms2g -Xmx2g -XX:+UseG1GC"
+    ports:
+    - "8080:8080"
+    depends_on:
+    - db
+volumes:
+  db-data: