Credentials (#7)

* initial commit on branch

* removing mongoDB from docker-compose for now

* serve participants credentials

* tidy up by removing some comments

* tweaks in response to code review

* tweaks

* remove duplicate text in README

* adjust local run command to include mongo

* update README to reflect CLI command

* change find query to find_one, and exclude _id from result

Co-authored-by: David <[email protected]>

.env.example

@@ -5,4 +5,13 @@ AIRFLOW_SERVER="airflow-webserver"
 # UCAM API
 UCAM_URI=""
 UCAM_USERNAME=""
-UCAM_PASSWORD=""
+UCAM_PASSWORD=""
+
+# --- USERS ---
+#   for local development, when changing log in values
+#   be sure to clean the docker volumes before rebooting
+_MONGO_INITDB_ROOT_USERNAME=""
+_MONGO_INITDB_ROOT_PASSWORD=""
+_MONGO_INITDB_DATABASE="patient_credentials"
+_MONGO_INITDB_COLLECTION="credentials"
+_MONGO_HOST="mongo_credentials"

.gitignore

@@ -17,4 +17,5 @@ requirements.txt
 .nox
 
 # Possible remnants of local dev
-/api/docs
+/api/docs
+/dist/*

README.md

@@ -34,6 +34,7 @@ docker-compose -f example.docker-compose.yml up
 
 Open your browser and try out a few endpoints, e.g.
 - http://localhost/patients
+- http://localhost/patients/credentials/{participant_id}
 - http://localhost/docs/axivity
 - http://localhost/status
 
@@ -61,11 +62,11 @@ A CLI command sets up the API locally to enable hot-reloading as code changes, s
 ```shell
 pyenv install 3.8.0 && pyenv global 3.8.0
 ```
-Add the required environmental variables in the `.env` file and quickstart the API which will watch for local changes:
+Add the required environmental variables in the `.env` file and quickstart the API which will watch for local changes. This will also spin up a docker container for the `mongodb` and patient credentials. Add the `--clean` command to auto-clean the docker volume when you shut down the API:
 
 ```shell
 poetry install
-poetry run local
+poetry run local # --clean
 ```
 
 #### GET /docs

api/patients.py

@@ -4,6 +4,7 @@
 
 from fastapi import APIRouter, Query
 
+from api.utils.db import PatientsCredentials, get_patients_credentials
 from api.utils.ucam import PatientWithDevices, get_one_patient, get_patients
 
 router = APIRouter()
@@ -35,6 +36,12 @@ def patients(
     return patients
 
 
+@router.get("/credentials/{id}", response_model=PatientsCredentials)
+def one_patients_credentials(id: str) -> Optional[PatientsCredentials]:
+    """Return list of all technology platform credentials for this patient"""
+    return get_patients_credentials(id)
+
+
 @router.get("/{id}", response_model=PatientWithDevices)
 def one_patient(id: str) -> Optional[PatientWithDevices]:
     """Get more details about a patient"""

api/utils/db.py

@@ -0,0 +1,41 @@
+import os
+from typing import Optional
+
+from dotenv import load_dotenv
+from pydantic.dataclasses import dataclass
+from pymongo import MongoClient
+
+load_dotenv()
+
+# setup mongodb connection
+myclient = MongoClient(
+    host=[f"{os.getenv('_MONGO_HOST')}:27017"],
+    username=os.getenv("_MONGO_INITDB_ROOT_USERNAME"),
+    password=os.getenv("_MONGO_INITDB_ROOT_PASSWORD"),
+)
+mydb = myclient[os.getenv("_MONGO_INITDB_DATABASE")]
+mycol = mydb[os.getenv("_MONGO_INITDB_COLLECTION")]
+
+
+@dataclass
+class PatientsCredentials:
+    """Patient credentials"""
+
+    patient_id: str
+    dreem_email: str
+    dreem_password: str
+    wildkeys_email: str
+    wildkeys_password: str
+    tfa_email: str
+    tfa_password: str
+
+
+def get_patients_credentials(the_id: str) -> Optional[PatientsCredentials]:
+    """Get credentials for one patient based on the ID"""
+    myquery = {"patient_id": the_id}
+    payload = mycol.find_one(myquery, {"_id": 0})  # exclude _id from result
+    if payload:
+        patient_credentials = PatientsCredentials(**payload)
+        return patient_credentials
+    else:
+        return None

cli.py

@@ -135,7 +135,8 @@ def version() -> None:
 
 
 @cli.command()
-def run_local() -> None:
+@click.option("--clean", is_flag=True, help="removes volume afterwards")
+def run_local(clean: bool) -> None:
     """Run locally with adjusted settings and loaded .envs"""
     import os
 
@@ -144,9 +145,16 @@ def run_local() -> None:
 
     load_dotenv()
     os.environ["AIRFLOW_SERVER"] = "localhost"
+    os.environ["_MONGO_HOST"] = "localhost"
+
+    run_command("docker-compose -f example.docker-compose.yml up -d mongo")
 
     uvicorn.run("api.main:api", host="0.0.0.0", port=80, reload=True)  # noqa: S104
 
+    run_command(
+        f"docker-compose -f example.docker-compose.yml down {'-v' if clean else ''}"
+    )  # cleanup
+
 
 if __name__ == "__main__":
     cli()

example.docker-compose.yml

@@ -12,3 +12,19 @@ services:
       - .env
     volumes:
       - ./ssh:/root/.ssh
+
+  mongo:
+    container_name: mongo_credentials
+    image: mongo:5.0
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: ${_MONGO_INITDB_ROOT_USERNAME}
+      MONGO_INITDB_ROOT_PASSWORD: ${_MONGO_INITDB_ROOT_PASSWORD}
+      MONGO_INITDB_DATABASE: ${_MONGO_INITDB_DATABASE}
+    ports:
+      - '27017:27017'
+    volumes:
+      - mongo-db-volume:/data/db
+      - ./init/mongo-init.sh:/docker-entrypoint-initdb.d/mongo-init.sh:ro
+
+volumes:
+  mongo-db-volume: null

init/mongo-init.sh

@@ -0,0 +1,14 @@
+set -e
+
+mongo <<EOF
+use $MONGO_INITDB_DATABASE
+
+db.createUser({
+  user: '$MONGO_INITDB_ROOT_USERNAME',
+  pwd: '$MONGO_INITDB_ROOT_PASSWORD',
+  roles: [{
+    role: 'readWrite',
+    db: '$MONGO_INITDB_DATABASE'
+  }]
+})
+EOF

pyproject.toml

@@ -11,6 +11,7 @@ fastapi = "^0.70.1"
 uvicorn = "^0.16.0"
 requests = "^2.27.0"
 pydantic = "^1.9.0"
+pymongo = "^4.0.1"
 
 [tool.poetry.dev-dependencies]
 pre-commit = "^2.16.0"