Add External integration tests

integration_test/.gitignore

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+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
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+*.egg
+MANIFEST
+
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+
+# Installer logs
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+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
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+
+# pyenv
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+# pipenv
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+
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+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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+### Python Patch ###
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+
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+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python

integration_test/Dockerfile

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+# Use an official Python runtime as a parent image
+FROM python:3.9-slim
+
+# Set the working directory in the container
+WORKDIR /app
+
+# Copy the requirements file into the container
+COPY requirements.txt .
+
+# Install dependencies
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Copy the rest of the application into the container
+COPY . .
+
+# Default command to run tests
+CMD ["pytest"]

integration_test/README.md

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+# Integration Tests
+
+Integration tests for fEMR. This project will bring up the entire fEMR stack with docker then run tests against it.
+
+Assumes that the femr docker container's name is `femr-femr`, otherwise you will need to re-build it with the new name.
+
+## Run with Docker
+
+Ensure that the femr container is built with name `femr-femr`, before running the tests.
+
+In the `integration-test` directory, run the tests with:
+
+```bash
+docker compose up --build
+```
+
+## Build Image
+
+In the root of the fEMR repository:
+
+```bash
+docker compose build
+```

integration_test/conftest.py

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+from testcontainers.mysql import MySqlContainer
+from testcontainers.selenium import BrowserWebDriverContainer
+from selenium.webdriver import DesiredCapabilities
+from testcontainers.core.container import DockerContainer
+from testcontainers.core.network import Network
+from testcontainers.core.waiting_utils import wait_for_logs
+
+from testcontainers.core.image import DockerImage
+import socket
+from contextlib import closing
+import requests
+import time
+import docker
+import os
+import re
+
+client = docker.from_env()
+
+try:
+    femr_image = os.getenv("FEMR_IMAGE_NAME", "femr-femr")
+
+    # Verify Image exists
+    client.images.get(femr_image)
+except:
+    femr_image = None
+
+assert femr_image is not None, "FEMR image not found, build image to 'femr-femr' or set FEMR_IMAGE_NAME environment variable to the correct image name"
+
+sql_container_spec = MySqlContainer('mysql:9.1.0', "femr", "password", "password", "femr_db", 3306)\
+    .with_network_aliases("mysql")\
+    .with_command("mysqld --log-bin-trust-function-creators=1")
+
+
+import pytest
+
+@pytest.fixture(scope='module', autouse=True)
+def run_before_and_after_tests(request):
+    """Fixture to execute asserts before and after a test is run"""
+
+    network_name = "femr_test_network" + str(time.time())
+    network = client.networks.create(network_name, driver="bridge")
+
+    def cleanup():
+        network.remove()
+
+    request.addfinalizer(cleanup)
+
+    with sql_container_spec as mysql:
+        network.connect(mysql._container.id, aliases=["db"])
+
+        femr_container_spec = DockerContainer(femr_image)\
+            .with_bind_ports("9000", "9000")\
+            .with_env("DB_URL", f'jdbc:mysql://db:3306/femr_db?characterEncoding=UTF-8&useSSL=false&allowPublicKeyRetrieval=true')\
+            .with_env("DB_USER", 'femr')\
+            .with_env("DB_PASS", 'password')\
+            .with_env("IS_DOCKER",'true')
+
+
+
+        with femr_container_spec as femr_container:
+            network.connect(femr_container_spec._container.id, aliases=["femr"])
+
+            wait_for_logs(femr_container, re.compile(".*Listening for HTTP on.*", flags=re.DOTALL | re.MULTILINE).search)
+
+            print("Femr Started")
+
+            femr_address = f"http://{femr_container.get_container_host_ip()}:{femr_container.get_exposed_port(9000)}"
+            os.environ["FEMR_ADDRESS"] = femr_address
+
+            yield
+
+
+@pytest.fixture(scope='session', autouse=True)
+def setup_selenium_container():
+    with BrowserWebDriverContainer(DesiredCapabilities.CHROME) as selenium_container:
+        os.environ["SELENIUM_ADDRESS"] = selenium_container.get_connection_url()
+        yield

integration_test/pyproject.toml

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+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]

integration_test/requirements.txt

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+testcontainers==4.9.0
+pytest==8.3.4
+selenium==4.27.1

integration_test/tests/test_basic_functionality.py

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+import pytest
+import time
+import json
+from selenium import webdriver
+from selenium.webdriver.common.by import By
+from selenium.webdriver.common.action_chains import ActionChains
+from selenium.webdriver.support import expected_conditions
+from selenium.webdriver.support.wait import WebDriverWait
+from selenium.webdriver.common.keys import Keys
+from selenium.webdriver.common.desired_capabilities import DesiredCapabilities
+import os
+import requests
+
+
+def test_femr_is_alive():
+    femr_address = os.getenv("FEMR_ADDRESS")
+
+    assert femr_address is not None, "FEMR_ADDRESS environment variable not set"
+
+    response = requests.get(femr_address)
+    assert response.status_code == 200
+
+def test_can_login_and_logout_to_admin():
+    femr_address = os.getenv("FEMR_ADDRESS")
+
+    assert femr_address is not None, "FEMR_ADDRESS environment variable not set"
+
+    driver_address = os.getenv("SELENIUM_ADDRESS")
+
+    assert driver_address is not None, "SELENIUM_ADDRESS environment variable not set"
+
+    driver = webdriver.Remote(command_executor=driver_address, options=webdriver.ChromeOptions())
+
+    driver.get(f"{femr_address}/")
+
+    # Test Login
+    driver.set_window_size(1361, 1157)
+    driver.find_element(By.NAME, "email").click()
+    driver.find_element(By.NAME, "email").send_keys("admin")
+    driver.find_element(By.NAME, "password").send_keys("admin")
+    driver.find_element(By.CSS_SELECTOR, "input:nth-child(4)").click()
+    assert "Welcome to fEMR" in driver.find_element(By.ID, "home_index_h2_Welcome").text
+
+    # Test Logout
+    driver.find_element(By.CSS_SELECTOR, ".glyphicon-log-out").click()
+    assert driver.find_element(By.CSS_SELECTOR, "h1").text == "Please sign in"
+

requirements.txt

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+testcontainers==4.8.2