first commit

.github/PULL_REQUEST_TEMPLATE.md

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+<!-- This is based on openmrs-cord PR template. -->
+
+## Description of what I changed
+
+<!--- Describe your changes in detail -->
+<!--- It can simply be your commit message, which you must have -->
+<!--- If your PR is related to an issue , please mention it here. -->
+<!--- It is generally a good practice to first file an issue with enough
+  context and reference it in the PR, but if you don't have that, please remove
+  this section. -->
+
+## E2E test
+
+<!-- There are different scenarios for using the tools in this repo; please
+  help your reviewers by describing how you have e2e tested your change. -->
+
+TESTED:
+
+Please replace this with a description of how you tested your PR beyond the
+automated e2e/unit tests.
+
+## Checklist: I completed these to help reviewers :)
+
+<!--- Put an `x` in the box if you did the task -->
+<!--- If you forgot a task please follow the instructions below -->
+
+- [ ] I have read and will follow the [review process](https://github.com/GoogleCloudPlatform/openmrs-fhir-analytics/blob/master/doc/review_process.md).
+- [ ] I am familiar with Google Style Guides for the language I have coded in.
+
+  No? Please take some time and review [Java](https://google.github.io/styleguide/javaguide.html) and [Python](https://google.github.io/styleguide/pyguide.html) style guides.
+
+- [ ] My IDE is configured to follow the Google [**code styles**](https://google.github.io/styleguide/).
+
+  No? Unsure? -> [configure your IDE](https://github.com/google/google-java-format).
+
+- [ ] I have **added tests** to cover my changes. (If you refactored existing code that was well tested you do not have to add tests)
+- [ ] I ran `mvn clean package` right before creating this pull request and added all formatting changes to my commit.
+- [ ] All new and existing **tests passed**.
+- [ ] My pull request is **based on the latest changes** of the master branch.
+
+  No? Unsure? -> execute command `git pull --rebase upstream master`

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "maven"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # Allow up to 30 open pull requests at the same time
+    open-pull-requests-limit: 30

.github/workflows/codecov.yml

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+# 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: 17
+    - 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

.github/workflows/codeql.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  schedule:
+    - cron: '25 21 * * 6'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby', 'swift' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - uses: actions/setup-java@v4
+      with:
+        distribution: 'temurin'
+        java-version: '17'
+
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.gitignore

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+**/target/
+/tmp/
+
+# IntelliJ
+.idea/
+*.iml
+
+# Local configuration file (sdk path, etc)
+local.properties
+
+# VSCode/Eclipse project files
+.vscode
+.classpath
+.project
+.settings
+bin/
+gen/
+
+# Python cache files
+__pycache__/
+
+# MacOS
+.DS_Store

CONTRIBUTING.md

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+# How to Contribute
+
+We'd love to accept your patches and contributions to this project. There are
+just a few small guidelines you need to follow.
+
+## Contributor License Agreement
+
+Contributions to this project must be accompanied by a Contributor License
+Agreement (CLA). You (or your employer) retain the copyright to your
+contribution; this simply gives us permission to use and redistribute your
+contributions as part of the project. Head over to
+<https://cla.developers.google.com/> to see your current agreements on file or
+to sign a new one.
+
+You generally only need to submit a CLA once, so if you've already submitted one
+(even if it was for a different project), you probably don't need to do it
+again.
+
+## Code reviews
+
+All submissions by non-project members, require review. We use GitHub pull
+requests for this purpose. Consult
+[GitHub Help](https://help.github.com/articles/about-pull-requests/) for more
+information on using pull requests. We use GitHub for issue tracking.
+
+## Community Guidelines
+
+This project follows
+[Google's Open Source Community Guidelines](https://opensource.google/conduct/).

Dockerfile

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+#
+# 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.
+#
+
+# Image for building and running tests against the source code of
+# the FHIR Gateway.
+FROM maven:3.8.7-eclipse-temurin-17-focal as build
+
+RUN apt-get update && apt-get install -y nodejs npm
+RUN npm cache clean -f && npm install -g n && n stable
+
+WORKDIR /app
+
+COPY server/src ./server/src
+COPY server/pom.xml ./server/
+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 .
+
+RUN mvn spotless:check
+# Updating license will fail in e2e and there is no point doing it here anyways.
+RUN mvn --batch-mode package -Dlicense.skip=true
+
+
+# Image for FHIR Gateway binary with configuration knobs as environment vars.
+FROM eclipse-temurin:17-jdk-focal as main
+
+COPY --from=build /app/exec/target/fhir-gateway-exec.jar /
+COPY resources/hapi_page_url_allowed_queries.json resources/hapi_page_url_allowed_queries.json
+
+ENV PROXY_PORT=8080
+ENV TOKEN_ISSUER="http://localhost/auth/realms/test"
+ENV PROXY_TO="http://localhost:8099/fhir"
+ENV BACKEND_TYPE="HAPI"
+
+# If ACCESS_CHECKER is set to a non-empty value, patient level access checks
+# are enabled; otherwise any valid token issued by TOKEN_ISSUER can be used
+# for full access to the FHIR store.
+ENV ACCESS_CHECKER="list"
+ENV RUN_MODE="PROD"
+
+ENTRYPOINT java -jar fhir-gateway-exec.jar --server.port=${PROXY_PORT}