Merge branch 'main' into dependabot/maven/com.google.http-client-goog…

…le-http-client-gson-1.44.1

.github/workflows/codecov.yml

@@ -0,0 +1,25 @@
+# This is based on:
+# https://github.com/codecov/example-java-maven/blob/main/.github/workflows/ci.yml
+name: Codecov
+on: [push, pull_request]
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Set up JDK 11
+      uses: actions/setup-java@v1
+      with:
+        java-version: 11
+    - name: Install dependencies
+      run: mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V
+    - name: Run tests and collect coverage
+      run: mvn -B test
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        # To find this token, and how it is stored in the repo, see:
+        # https://docs.codecov.com/docs/adding-the-codecov-token
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: google/fhir-gateway

Dockerfile

@@ -29,6 +29,7 @@ COPY plugins/src ./plugins/src
 COPY plugins/pom.xml ./plugins/
 COPY exec/src ./exec/src
 COPY exec/pom.xml ./exec/
+COPY coverage/pom.xml ./coverage/
 COPY license-header.txt .
 COPY pom.xml .
 

README.md

@@ -3,6 +3,7 @@
 <!-- Build status of the main branch -->
 
 [![Build Status](https://storage.googleapis.com/fhir-proxy-build-badges/build.svg)](https://storage.googleapis.com/fhir-proxy-build-badges/build.html)
+[![codecov](https://codecov.io/gh/google/fhir-gateway/branch/main/graph/badge.svg)](https://app.codecov.io/gh/google/fhir-gateway/tree/main)
 
 FHIR Information Gateway is a simple access-control proxy that sits in front of
 a [FHIR](https://www.hl7.org/fhir/) store (e.g., a

coverage/pom.xml

@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Copyright 2021-2024 Google LLC
+
+    Licensed under the Apache License, Version 2.0 (the "License");
+    you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+          http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software
+    distributed under the License is distributed on an "AS IS" BASIS,
+    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+    See the License for the specific language governing permissions and
+    limitations under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+    http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <parent>
+    <groupId>com.google.fhir.gateway</groupId>
+    <artifactId>fhir-gateway</artifactId>
+    <version>0.3.2</version>
+  </parent>
+
+  <groupId>com.google.fhir.gateway</groupId>
+  <artifactId>coverage</artifactId>
+  <name>coverage</name>
+  <description>Compute aggregated test code coverage</description>
+  <packaging>pom</packaging>
+
+  <properties>
+    <maven.deploy.skip>true</maven.deploy.skip>
+    <root.basedir>${project.parent.basedir}</root.basedir>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>com.google.fhir.gateway</groupId>
+      <artifactId>server</artifactId>
+      <version>${project.parent.version}</version>
+    </dependency>
+
+    <dependency>
+      <groupId>com.google.fhir.gateway</groupId>
+      <artifactId>plugins</artifactId>
+      <version>${project.parent.version}</version>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>report-aggregate</id>
+            <phase>test</phase>
+            <goals>
+              <goal>report-aggregate</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+
+</project>

doc/design.md

@@ -553,10 +553,11 @@ In the main text, we refer to these examples by "all-patients",
 ## Notes
 
 [^1]:
-  The simplified
-  [Implicit](https://smilecdr.com/docs/smart/smart_on_fhir_authorization_flows.html#launch-flow-implicit-grant)
-  flow could work for our use-case too but that has important security
-  shortcomings. For example, it exposes access_token in URLs which can leak
-  through browser history. Another more important shortcoming is that we cannot
-  implement PKCE in the Implicit flow as the access_token is directly returned
-  in the first request.
+
+The simplified
+[Implicit](https://smilecdr.com/docs/smart/smart_on_fhir_authorization_flows.html#launch-flow-implicit-grant)
+flow could work for our use-case too but that has important security
+shortcomings. For example, it exposes access_token in URLs which can leak
+through browser history. Another more important shortcoming is that we cannot
+implement PKCE in the Implicit flow as the access_token is directly returned in
+the first request.

pom.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
 
-    Copyright 2021-2023 Google LLC
+    Copyright 2021-2024 Google LLC
 
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.
@@ -46,6 +46,7 @@
     <module>exec</module>
     <module>plugins</module>
     <module>server</module>
+    <module>coverage</module>
   </modules>
 
   <scm>
@@ -128,7 +129,7 @@
     <dependency>
       <groupId>org.mockito</groupId>
       <artifactId>mockito-core</artifactId>
-      <version>5.8.0</version>
+      <version>5.11.0</version>
       <scope>test</scope>
     </dependency>
 
@@ -147,14 +148,27 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.11.0</version>
+          <version>3.13.0</version>
           <configuration>
             <release>11</release>
           </configuration>
         </plugin>
       </plugins>
     </pluginManagement>
+
     <plugins>
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <version>0.8.11</version>
+        <executions>
+          <execution>
+            <goals>
+              <goal>prepare-agent</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
       <plugin>
         <groupId>com.mycila</groupId>
         <artifactId>license-maven-plugin</artifactId>

server/pom.xml

@@ -82,7 +82,7 @@
     <dependency>
       <groupId>com.google.http-client</groupId>
       <artifactId>google-http-client</artifactId>
-      <version>1.43.3</version>
+      <version>1.44.1</version>
     </dependency>
 
     <dependency>