Merge pull request #184 from FirelyTeam/r4/develop

Release 1.3 R4

* [#171 - Rewrite IndexService to use FhirPath expressions](#171)
  * Fixes #30 
  * Fixes #155
* [#157 - Migrated Spark.Engine and Spark.Mongo to netstandard2.0](#157)
  * Fixes #45
* [#134 - Spark.Web - small  web project made available as an .NET Core example](#134)
* [#79 - HTML view renders too much white space](#79)
* [#80 - HTML view OperationOutcome not rendered](#80)
* [#19 - Posting to an id with a dot gives 404](#19)
* Spark.Engine and Spark.Mongo available as NuGet packages
* Docker image

.dockerignore

@@ -0,0 +1 @@
+.vs/

.editorconfig

@@ -0,0 +1,12 @@
+# EditorConfig
+# https://docs.microsoft.com/en-us/visualstudio/ide/editorconfig-code-style-settings-reference?view=vs-2017
+
+root = true
+
+# Ensure space is used for indentation in all files
+[*]
+indent_style = space
+
+# Code files indentation
+[*.{cs,csx}]
+indent_size = 4

.gitignore

@@ -220,3 +220,9 @@ _Pvt_Extensions
 #NDepend
 NDependOut/
 *.ndproj
+
+# OS X files
+.DS_Store
+
+# VS Code
+.vscode/

.travis.yml

@@ -0,0 +1,22 @@
+language: node_js
+node_js:
+  - "stable"
+cache:
+  directories:
+  - node_modules
+before_script:
+  - "cd docs" 
+  - "npm install"
+script:
+  - "npm run test"
+after_success:
+  - "npm run deploy"
+deploy:
+  provider: pages
+  skip-cleanup: true
+  github-token: $GITHUB_TOKEN
+  local_dir: docs/public
+  target_branch: gh-pages
+  keep-history: true
+  on:
+    branch: develop

CONTRIBUTORS.md

@@ -17,3 +17,5 @@ Richard added GZip support
 Brian made the resources look fresh in the UI.
 
 * [Kenneth Myhra](https://github.com/kennethmyhra) - Kufu
+
+* [Ole Kristian Losvik](https://github.com/losolio)

Dockerfile

@@ -0,0 +1,23 @@
+FROM mcr.microsoft.com/dotnet/core/aspnet:2.2-stretch-slim AS base
+WORKDIR /app
+EXPOSE 80
+EXPOSE 443
+
+FROM mcr.microsoft.com/dotnet/core/sdk:2.2-stretch AS build
+WORKDIR /src
+COPY ["./src/Spark.Web/", "Spark.Web/"]
+COPY ["./src/Spark.Engine/", "Spark.Engine/"]
+COPY ["./src/Spark.Mongo/", "Spark.Mongo/"]
+RUN dotnet restore "/src/Spark.Web/Spark.Web.csproj"
+COPY . .
+RUN dotnet build "/src/Spark.Web/Spark.Web.csproj" -c Release -o /app
+
+FROM build AS publish
+RUN dotnet publish "/src/Spark.Web/Spark.Web.csproj" -c Release -o /app
+
+FROM base AS final
+WORKDIR /app
+COPY --from=publish /app .
+# COPY --from=build /src/Spark.Web/example_data/fhir_examples ./fhir_examples
+
+ENTRYPOINT ["dotnet", "Spark.Web.dll"]

LICENSE

@@ -1,4 +1,5 @@
-Copyright (c) 2018, Firely ([email protected]) and contributors
+Copyright (c) 2014 Firely ([email protected]),
+Copyright (c) 2018 Kufu ([email protected]) and contributors
 See the file CONTRIBUTORS for details
 
 All rights reserved.

README.md

@@ -12,6 +12,26 @@ Kufu and the community, will keep enhancing this server to support the latest ve
 We also welcome anyone who wants to support this effort and help us make Spark a better reference
 platform and playground for FHIR.
 
+**DISCLAIMER: The web projects Spark.Web and Spark.Classic are meant as reference implementations and should never be used out of the box in a production environment without adding as a minimum security features.**
+
+## Quickstart
+The easiest way to test Spark FHIR server is by using Docker. Make sure you have installed [Docker](https://docs.docker.com/install/). On Linux you will need to install [Docker Compose](https://docs.docker.com/compose/install/) as well. After installing Docker you could run Spark server by running the command for your operating system: 
+
+DSTU2:
+ * Mac OS X / Windows: `curl 'https://raw.githubusercontent.com/firelyteam/spark/develop/dockers/spark-dstu2/docker-compose.yml' > docker-compose.yml && docker-compose up`
+ * Linux: `curl 'https://raw.githubusercontent.com/FirelyTeam/spark/develop/dockers/spark-dstu2/docker-compose.yml' > docker-compose.yml && sudo docker-compose up`
+
+STU3:
+ * Mac OS X / Windows: `curl 'https://raw.githubusercontent.com/firelyteam/spark/develop/dockers/spark-stu3/docker-compose.yml' > docker-compose.yml && docker-compose up`
+ * Linux: `curl 'https://raw.githubusercontent.com/FirelyTeam/spark/develop/dockers/spark-stu3/docker-compose.yml' > docker-compose.yml && sudo docker-compose up`
+
+R4:
+ * Mac OS X / Windows: `curl 'https://raw.githubusercontent.com/firelyteam/spark/develop/dockers/spark-r4/docker-compose.yml' > docker-compose.yml && docker-compose up`
+ * Linux: `curl 'https://raw.githubusercontent.com/FirelyTeam/spark/develop/dockers/spark-r4/docker-compose.yml' > docker-compose.yml && sudo docker-compose up`
+
+Spark FHIR server will be available after startup at `http://localhost:5555`.
+
+## Versions
 
 #### DSTU1
 DSTU1 is no longer maintained by this project. The source code can be found in the branch **dstu1/master**.

Spark.sln

@@ -3,15 +3,17 @@ Microsoft Visual Studio Solution File, Format Version 12.00
 # Visual Studio 15
 VisualStudioVersion = 15.0.28307.329
 MinimumVisualStudioVersion = 10.0.40219.1
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Spark.Engine", "src\Spark.Engine\Spark.Engine.csproj", "{426991A6-546C-43D5-B055-A38D0175824F}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Spark.Engine", "src\Spark.Engine\Spark.Engine.csproj", "{426991A6-546C-43D5-B055-A38D0175824F}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Spark.Mongo", "src\Spark.Mongo\Spark.Mongo.csproj", "{5F0EAEA9-5226-46FF-A915-4DE9B3BA6ADD}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Spark.Mongo", "src\Spark.Mongo\Spark.Mongo.csproj", "{5F0EAEA9-5226-46FF-A915-4DE9B3BA6ADD}"
 EndProject
 Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Spark", "src\Spark\Spark.csproj", "{D12C6E96-4893-408E-9F53-A142DC82E993}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Spark.Engine.Test", "src\Spark.Engine.Test\Spark.Engine.Test.csproj", "{5CA90A21-AC2E-4C30-B618-A459A1E5B04F}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Spark.Engine.Test", "src\Spark.Engine.Test\Spark.Engine.Test.csproj", "{5CA90A21-AC2E-4C30-B618-A459A1E5B04F}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Spark.Mongo.Tests", "src\Spark.Mongo.Tests\Spark.Mongo.Tests.csproj", "{3D3C588D-6BB5-46CD-B844-61136D30A1FB}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Spark.Mongo.Tests", "src\Spark.Mongo.Tests\Spark.Mongo.Tests.csproj", "{3D3C588D-6BB5-46CD-B844-61136D30A1FB}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Spark.Web", "src\Spark.Web\Spark.Web.csproj", "{6A59CE4B-D912-4995-A805-89705B8134E0}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
@@ -39,6 +41,10 @@ Global
 		{3D3C588D-6BB5-46CD-B844-61136D30A1FB}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{3D3C588D-6BB5-46CD-B844-61136D30A1FB}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{3D3C588D-6BB5-46CD-B844-61136D30A1FB}.Release|Any CPU.Build.0 = Release|Any CPU
+		{6A59CE4B-D912-4995-A805-89705B8134E0}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{6A59CE4B-D912-4995-A805-89705B8134E0}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{6A59CE4B-D912-4995-A805-89705B8134E0}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{6A59CE4B-D912-4995-A805-89705B8134E0}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

docker-compose.yml

@@ -0,0 +1,39 @@
+version: "3"  
+services:  
+  spark:
+    container_name: spark
+    restart: always
+    build:
+      context: .
+      dockerfile: Dockerfile
+    environment:
+      - StoreSettings__ConnectionString=mongodb://root:CosmicTopSecret@mongodb:27017/spark?authSource=admin
+      - SparkSettings__Endpoint=http://localhost:5555/fhir
+    ports:
+      - "5555:80"
+      - "44348:443"
+    links:
+      - mongodb
+    depends_on:
+      - mongodb
+  mongodb:
+    container_name: mongodb
+    image: mongo
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: CosmicTopSecret
+    ports:
+      - "17017:27017"
+  mongosetup:
+    container_name: mongosetup
+    image: mongo
+    volumes:
+      - ./src/Spark.Web/example_data/db_dump:/data/db_dump
+    depends_on:
+      - mongodb
+    links:
+      - mongodb
+    entrypoint:
+      ["mongorestore", "--uri=mongodb://root:CosmicTopSecret@mongodb:27017/spark", "--drop", "--archive=/data/db_dump/r4.archive.gz", "--gzip"]
+    environment:
+      WAIT_HOSTS: mongodb:27017

dockers/Updating_docker_images.md

@@ -0,0 +1,24 @@
+# Dockers and docker composers
+
+## Update Spark images on Docker hub
+
+In project root folder for each of the branches `develop`, `stu3/develop` and `r4/develop`: 
+
+```bash
+docker build -t spark-version .
+docker tag spark-fhirversion sparkfhir/spark-fhirversion
+docker login
+docker push sparkfhir/spark-fhirversion
+```
+
+## Updating Mongo images with preloaded examples on Docker Hub
+
+In each `dockers/mongo-spark-fhirversion directory`:
+
+```bash
+docker build -t mongo-spark-fhirversion .
+docker tag mongo-spark-fhirversion sparkfhir/mongo-spark-fhirversion:pre-release
+docker login
+docker push sparkfhir/mongo-spark-fhirversion:pre-release
+```
+

dockers/mongo-spark-dstu2/Dockerfile

@@ -0,0 +1,3 @@
+FROM mongo
+COPY dstu2.archive.gz /home/
+COPY mongorestore.sh /docker-entrypoint-initdb.d/

dockers/mongo-spark-dstu2/mongorestore.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+mongorestore --drop --archive=/home/dstu2.archive.gz --gzip 

dockers/mongo-spark-r4/Dockerfile

@@ -0,0 +1,3 @@
+FROM mongo
+COPY r4.archive.gz /home/
+COPY mongorestore.sh /docker-entrypoint-initdb.d/

dockers/mongo-spark-r4/mongorestore.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+mongorestore --drop --archive=/home/r4.archive.gz --gzip

dockers/mongo-spark-stu3/Dockerfile

@@ -0,0 +1,3 @@
+FROM mongo
+COPY stu3.archive.gz /home/
+COPY mongorestore.sh /docker-entrypoint-initdb.d/

dockers/mongo-spark-stu3/mongorestore.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+mongorestore --drop --archive=/home/stu3.archive.gz --gzip

dockers/spark-dstu2/docker-compose.yml

@@ -0,0 +1,22 @@
+version: "3"  
+services:  
+  spark:
+    container_name: spark
+    restart: always
+    image: sparkfhir/spark-dstu2:pre-release
+    environment:
+      - StoreSettings__ConnectionString=mongodb://root:CosmicTopSecret@mongodb:27017/spark?authSource=admin
+      - SparkSettings__Endpoint=http://localhost:5555/fhir
+    ports:
+      - "5555:80"
+      - "44344:443"
+    depends_on:
+      - mongodb
+  mongodb:
+    container_name: mongodb
+    image: sparkfhir/mongo-spark-dstu2
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: CosmicTopSecret
+    ports:
+      - "17017:27017"

dockers/spark-r4/docker-compose.yml

@@ -0,0 +1,22 @@
+version: "3"  
+services:  
+  spark:
+    container_name: spark
+    restart: always
+    image: sparkfhir/spark-r4:pre-release
+    environment:
+      - StoreSettings__ConnectionString=mongodb://root:CosmicTopSecret@mongodb:27017/spark?authSource=admin
+      - SparkSettings__Endpoint=http://localhost:5555/fhir
+    ports:
+      - "5555:80"
+      - "44344:443"
+    depends_on:
+      - mongodb
+  mongodb:
+    container_name: mongodb
+    image: sparkfhir/mongo-spark-r4
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: CosmicTopSecret
+    ports:
+      - "17017:27017"

dockers/spark-stu3/docker-compose.yml

@@ -0,0 +1,22 @@
+version: "3"  
+services:  
+  spark:
+    container_name: spark
+    restart: always
+    image: sparkfhir/spark-stu3:pre-release
+    environment:
+      - StoreSettings__ConnectionString=mongodb://root:CosmicTopSecret@mongodb:27017/spark?authSource=admin
+      - SparkSettings__Endpoint=http://localhost:5555/fhir
+    ports:
+      - "5555:80"
+      - "44344:443"
+    depends_on:
+      - mongodb
+  mongodb:
+    container_name: mongodb
+    image: sparkfhir/mongo-spark-stu3
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: CosmicTopSecret
+    ports:
+      - "17017:27017"