From 6e14458f29bc6a41d87b5f59789ef0909d129345 Mon Sep 17 00:00:00 2001
From: yaso-meth <yasienmeth@gmail.com>
Date: Wed, 24 Jul 2024 13:20:52 +0200
Subject: [PATCH] update fastapi to guvicorn and improve supertoken integration

---
 backend/Dockerfile                | 32 +++++++++++++++--
 backend/__init__.py               | 53 +++++++++++++--------------
 backend/main.py                   | 59 ++++++++++++++++++++-----------
 backend/requirements.txt          |  2 +-
 backend/routers/docOffices.py     | 11 +++---
 backend/routers/patients.py       | 19 +++++-----
 backend/routers/patients_files.py | 11 +++---
 backend/routers/patients_notes.py | 13 +++----
 backend/routers/users.py          | 13 +++----
 docker-compose.yml                | 14 +++++---
 10 files changed, 142 insertions(+), 85 deletions(-)

diff --git a/backend/Dockerfile b/backend/Dockerfile
index 72c6fb7a..05489ec1 100644
--- a/backend/Dockerfile
+++ b/backend/Dockerfile
@@ -1,6 +1,32 @@
-FROM python:3.12-slim
+FROM tiangolo/uvicorn-gunicorn-fastapi:python3.11-slim AS builder
 
 WORKDIR /app
 
-COPY ./requirements.txt ./
-RUN pip3 install --no-cache-dir -r requirements.txt
\ No newline at end of file
+COPY requirements.txt ./
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip install -r requirements.txt
+
+# COPY . ./app
+
+# FROM builder as dev-envs
+
+# RUN <<EOF
+# apt-get update
+# apt-get install -y --no-install-recommends git
+# EOF
+
+# RUN <<EOF
+# useradd -s /bin/bash -m vscode
+# groupadd docker
+# usermod -aG docker vscode
+# EOF
+# # install Docker tools (cli, buildx, compose)
+# COPY --from=gloursdocker/docker / /
+
+# FROM python:3.12-slim
+
+# WORKDIR /app
+
+# COPY ./requirements.txt ./
+
+# RUN pip3 install --no-cache-dir -r requirements.txt
\ No newline at end of file
diff --git a/backend/__init__.py b/backend/__init__.py
index 4097a68f..51d9c310 100644
--- a/backend/__init__.py
+++ b/backend/__init__.py
@@ -1,27 +1,28 @@
-from supertokens_python import init, InputAppInfo, SupertokensConfig
-from supertokens_python.recipe import emailpassword, session, dashboard
+# from supertokens_python import init, InputAppInfo, SupertokensConfig
+# from supertokens_python.recipe import emailpassword, session, dashboard
 
-init(
-    app_info=InputAppInfo(
-        app_name="MIH_API_HUB",
-        api_domain="http://localhost:8080/",
-        website_domain="http://mzansi-innovation-hub.co.za",
-        api_base_path="/auth",
-        website_base_path="/auth"
-    ),
-    supertokens_config=SupertokensConfig(
-        # https://try.supertokens.com is for demo purposes. Replace this with the address of your core instance (sign up on supertokens.com), or self host a core.
-        connection_uri="http://MIH-SuperTokens:3567/",
-        api_key="leatucczyixqwkqqdrhayiwzeofkltds"
-    ),
-    framework='fastapi',
-    recipe_list=[
-        session.init(), # initializes session features
-        emailpassword.init(),
-        dashboard.init(admins=[
-            "yasienmeth@gmail.com",
-          ],
-        )
-    ],
-    mode='asgi' # use wsgi if you are running using gunicorn
-)
\ No newline at end of file
+# init(
+#     app_info=InputAppInfo(
+#         app_name="MIH_API_HUB",
+#         api_domain="http://localhost:8080/",
+#         website_domain="http://mzansi-innovation-hub.co.za",
+#         api_base_path="/auth",
+#         website_base_path="/auth"
+#     ),
+#     supertokens_config=SupertokensConfig(
+#         # https://try.supertokens.com is for demo purposes. Replace this with the address of your core instance (sign up on supertokens.com), or self host a core.
+#         connection_uri="supertokens:3567/",
+#         api_key="leatucczyixqwkqqdrhayiwzeofkltds"
+#     ),
+#     framework='fastapi',
+#     recipe_list=[
+#         # SuperTokens.init(),
+#         session.init(), # initializes session features
+#         emailpassword.init(),
+#         dashboard.init(admins=[
+#             "yasienmeth@gmail.com",
+#           ],
+#         )
+#     ],
+#     mode='wsgi' # use wsgi instead of asgi if you are running using gunicorn
+# )
\ No newline at end of file
diff --git a/backend/main.py b/backend/main.py
index f4c76fbf..ee5f14c5 100644
--- a/backend/main.py
+++ b/backend/main.py
@@ -1,21 +1,22 @@
 from fastapi import FastAPI, HTTPException
 from pydantic import BaseModel
-from .routers import docOffices, patients, patients_files, patients_notes, users, fileStorage, medicine
+# from .routers import docOffices, patients, patients_files, patients_notes, users, fileStorage, medicine
+import routers.docOffices as docOffices
+import routers.patients as patients
+import routers.patients_files as patients_files
+import routers.patients_notes as patients_notes
+import routers.users as users
+import routers.fileStorage as fileStorage
+import routers.medicine as medicine
+
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.middleware import Middleware
 from supertokens_python import get_all_cors_headers
 from supertokens_python.framework.fastapi import get_middleware
-from supertokens_python.recipe.session.framework.fastapi import verify_session
-from supertokens_python.recipe.session import SessionContainer
-from fastapi import Depends
 
-from supertokens_python.recipe.session.framework.fastapi import verify_session
-from supertokens_python.recipe.thirdparty.asyncio import (
-    get_user_by_id as get_user_by_id_thirdparty,
-)
-from supertokens_python.recipe.passwordless.asyncio import (
-    get_user_by_id as get_user_by_id_passwordless,
-)
+from supertokens_python import init, InputAppInfo, SupertokensConfig
+from supertokens_python.recipe import emailpassword, session, dashboard
+
 
 origins = [
     "http://localhost",
@@ -27,15 +28,31 @@ origins = [
     "*",
 ]
 
-# middleware = [
-#     Middleware(
-#     CORSMiddleware,
-#     allow_origins=origins,
-#     allow_credentials=True,
-#     allow_methods=["GET", "PUT", "POST", "DELETE", "OPTIONS", "PATCH"],
-#     allow_headers=["Content-Type"] + get_all_cors_headers(),
-#     )
-# ]
+init(
+    app_info=InputAppInfo(
+        app_name="MIH_API_HUB",
+        api_domain="http://localhost:8080/",
+        website_domain="http://mzansi-innovation-hub.co.za",
+        api_base_path="/auth",
+        website_base_path="/auth"
+    ),
+    supertokens_config=SupertokensConfig(
+        # https://try.supertokens.com is for demo purposes. Replace this with the address of your core instance (sign up on supertokens.com), or self host a core.
+        connection_uri="http://MIH-SuperTokens:3567/",
+        api_key="leatucczyixqwkqqdrhayiwzeofkltds"
+    ),
+    framework='fastapi',
+    recipe_list=[
+        # SuperTokens.init(),
+        session.init(), # initializes session features
+        emailpassword.init(),
+        dashboard.init(admins=[
+            "yasienmeth@gmail.com",
+          ],
+        )
+    ],
+    mode='wsgi' # use wsgi instead of asgi if you are running using gunicorn
+)
 
 app = FastAPI()#middleware=middleware)
 app.add_middleware(get_middleware())
@@ -81,6 +98,6 @@ def read_root():
 #         print(thirdparty_user)
 
 def serverRunning():
-    return {"Status": "Server is Up and Running"}
+    return {"Status": "Server is Up and Running. whats good in the hood"}
 
 
diff --git a/backend/requirements.txt b/backend/requirements.txt
index 519c8119..694a5bb0 100644
--- a/backend/requirements.txt
+++ b/backend/requirements.txt
@@ -4,7 +4,7 @@ mysql-connector-python
 minio
 reportlab
 requests
-watchfiles==0.21.0
+watchfiles
 python-multipart
 xlrd
 supertokens-python
\ No newline at end of file
diff --git a/backend/routers/docOffices.py b/backend/routers/docOffices.py
index cd073d82..55322139 100644
--- a/backend/routers/docOffices.py
+++ b/backend/routers/docOffices.py
@@ -1,17 +1,20 @@
 import mysql.connector
 from fastapi import APIRouter, HTTPException
-from ..database import dbConnection
+#from ..database import dbConnection
+import database
 #SuperToken Auth from front end
 from supertokens_python.recipe.session.framework.fastapi import verify_session
 from supertokens_python.recipe.session import SessionContainer
 from fastapi import Depends
 
+import database.dbConnection
+
 router = APIRouter()
 
 # Get Doctors Office By ID
 @router.get("/docOffices/{docOffic_id}", tags="DocOffice")
 async def read_docOfficeByID(docOffic_id: int, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM doctor_offices WHERE iddoctor_offices=%s"
     cursor.execute(query, (docOffic_id,))
@@ -26,7 +29,7 @@ async def read_docOfficeByID(docOffic_id: int, session: SessionContainer = Depen
 # Get Doctors Office By user
 @router.get("/docOffices/user/{user}", tags="DocOffice")
 async def read_docOfficeByID(user: str, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM users WHERE email=%s"
     cursor.execute(query, (user,))
@@ -47,7 +50,7 @@ async def read_docOfficeByID(user: str, session: SessionContainer = Depends(veri
 # Get List of all Doctors Office
 @router.get("/docOffices/", tags="DocOffice")
 async def read_All_DoctorsOffice(session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM doctor_offices"
     cursor.execute(query)
diff --git a/backend/routers/patients.py b/backend/routers/patients.py
index 615a75fe..e30a670e 100644
--- a/backend/routers/patients.py
+++ b/backend/routers/patients.py
@@ -1,7 +1,8 @@
 import mysql.connector
 from fastapi import APIRouter, HTTPException
 from pydantic import BaseModel
-from ..database import dbConnection
+#from ..database import dbConnection
+import database
 #SuperToken Auth from front end
 from supertokens_python.recipe.session.framework.fastapi import verify_session
 from supertokens_python.recipe.session import SessionContainer
@@ -46,7 +47,7 @@ class patientDeleteRequest(BaseModel):
 # Get Patient By ID Number
 @router.get("/patients/id/{pat_id}", tags="patients")
 async def read_patientByID(pat_id: str, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patients WHERE idpatients=%s"
     cursor.execute(query, (pat_id,))
@@ -71,7 +72,7 @@ async def read_patientByID(pat_id: str, session: SessionContainer = Depends(veri
 # Get Patient By ID Number
 @router.get("/patients/{id_no}", tags="patients")
 async def read_patientByID(id_no: str):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patients WHERE id_no=%s"
     cursor.execute(query, (id_no,))
@@ -95,7 +96,7 @@ async def read_patientByID(id_no: str):
 # Get List of all patients
 @router.get("/patients/user/{email}", tags="patients")
 async def read_all_patientsByUser(email: str, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     #query = "SELECT * FROM patients"
     query = "Select * from patients " 
@@ -129,7 +130,7 @@ async def read_all_patientsByUser(email: str, session: SessionContainer = Depend
 # Get List of all patients
 @router.get("/patients/", tags="patients")
 async def read_all_patients(session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patients"
     cursor.execute(query)
@@ -156,7 +157,7 @@ async def read_all_patients(session: SessionContainer = Depends(verify_session()
 # Get List of all patients by Doctors Office
 @router.get("/patients/docOffice/{docoff_id}", tags="patients")
 async def read_all_patientsby(docoff_id: str, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patients where doc_office_id=%s"
     cursor.execute(query, (docoff_id,))
@@ -183,7 +184,7 @@ async def read_all_patientsby(docoff_id: str, session: SessionContainer = Depend
 # Insert Patient into table
 @router.post("/patients/insert/", tags="patients", status_code=201)
 async def insertPatient(itemRequest : patientInsertRequest, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "insert into patients "
     query += "(id_no, first_name, last_name, email, cell_no, medical_aid, "
@@ -216,7 +217,7 @@ async def insertPatient(itemRequest : patientInsertRequest, session: SessionCont
 # Update Patient on table
 @router.put("/patients/update/", tags="patients")
 async def UpdatePatient(itemRequest : patientUpdateRequest, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "update patients "
     query += "set id_no=%s, first_name=%s, last_name=%s, email=%s, cell_no=%s, medical_aid=%s, "
@@ -251,7 +252,7 @@ async def UpdatePatient(itemRequest : patientUpdateRequest, session: SessionCont
 # delete Patient on table
 @router.delete("/patients/delete/", tags="patients")
 async def DeletePatient(itemRequest : patientDeleteRequest, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "delete from patients "
     query += "where id_no=%s and doc_office_id=%s"
diff --git a/backend/routers/patients_files.py b/backend/routers/patients_files.py
index 71350299..34553dc6 100644
--- a/backend/routers/patients_files.py
+++ b/backend/routers/patients_files.py
@@ -1,7 +1,8 @@
 import mysql.connector
 from fastapi import APIRouter, HTTPException
 from pydantic import BaseModel
-from ..database import dbConnection
+#from ..database import dbConnection
+import database
 from datetime import date
 #SuperToken Auth from front end
 from supertokens_python.recipe.session.framework.fastapi import verify_session
@@ -22,7 +23,7 @@ class fileInsertRequest(BaseModel):
 # Get List of all files
 @router.get("/files/patients/", tags="patients_files")
 async def read_all_files(session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patient_files"
     cursor.execute(query)
@@ -43,7 +44,7 @@ async def read_all_files(session: SessionContainer = Depends(verify_session())):
 # Get List of all files by patient
 @router.get("/files/patients/{patientID}", tags="patients_files")
 async def read_all_files_by_patient(patientID: int, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patient_files where patient_id = %s ORDER BY insert_date DESC"
     cursor.execute(query, (patientID,))
@@ -64,7 +65,7 @@ async def read_all_files_by_patient(patientID: int, session: SessionContainer =
 # Get List of all files by patient & DocOffice
 @router.get("/files/patients-docOffice/", tags="patients_files")
 async def read_all_files_by_patient(itemRequest: fileRequest, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "select patient_files.idpatient_files, patient_files.file_path, patient_files.file_name, patient_files.patient_id, patient_files.insert_date, patients.doc_office_id "
     query += "from patient_manager.patient_files "
@@ -92,7 +93,7 @@ async def read_all_files_by_patient(itemRequest: fileRequest, session: SessionCo
 @router.post("/files/insert/", tags="patients_notes", status_code=201)
 async def insertPatientFiles(itemRequest : fileInsertRequest, session: SessionContainer = Depends(verify_session())):
     today = date.today()
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "insert into patient_files "
     query += "(file_path, file_name, patient_id, insert_date) "
diff --git a/backend/routers/patients_notes.py b/backend/routers/patients_notes.py
index fdb48f9f..1c574fc9 100644
--- a/backend/routers/patients_notes.py
+++ b/backend/routers/patients_notes.py
@@ -2,7 +2,8 @@ import mysql.connector
 from fastapi import APIRouter, HTTPException
 from pydantic import BaseModel
 from datetime import date
-from ..database import dbConnection
+#from ..database import dbConnection
+import database
 #SuperToken Auth from front end
 from supertokens_python.recipe.session.framework.fastapi import verify_session
 from supertokens_python.recipe.session import SessionContainer
@@ -28,7 +29,7 @@ class patientNoteUpdateRequest(BaseModel):
 # Get List of all notes
 @router.get("/notes/patients/", tags="patients_notes")
 async def read_all_notes(session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patient_notes"
     cursor.execute(query)
@@ -48,7 +49,7 @@ async def read_all_notes(session: SessionContainer = Depends(verify_session())):
 # Get List of all notes by patient
 @router.get("/notes/patients/{patientID}", tags="patients_notes")
 async def read_all_patientsby(patientID: int, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM patient_notes where patient_id = %s ORDER BY insert_date DESC"
     cursor.execute(query, (patientID,))
@@ -69,7 +70,7 @@ async def read_all_patientsby(patientID: int, session: SessionContainer = Depend
 # Get List of all notes by patient
 @router.get("/notes/patients-docOffice/", tags="patients_notes")
 async def read_all_patientsby(itemRequest: fileRequest, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "select patient_notes.idpatient_notes, patient_notes.note_name, patient_notes.note_text, patient_notes.patient_id, patient_notes.insert_date, patients.doc_office_id "
     query += "from patient_manager.patient_notes "
@@ -94,7 +95,7 @@ async def read_all_patientsby(itemRequest: fileRequest, session: SessionContaine
 @router.post("/notes/insert/", tags="patients_notes", status_code=201)
 async def insertPatientNotes(itemRequest : patientNoteInsertRequest, session: SessionContainer = Depends(verify_session())):
     today = date.today()
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "insert into patient_notes "
     query += "(note_name, note_text, patient_id, insert_date) "
@@ -117,7 +118,7 @@ async def insertPatientNotes(itemRequest : patientNoteInsertRequest, session: Se
 @router.put("/notes/update/", tags="patients_notes")
 async def UpdatePatient(itemRequest : patientNoteUpdateRequest, session: SessionContainer = Depends(verify_session())):
     today = date.today()
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "update patient_notes "
     query += "set note_name=%s, note_text=%s, patient_id=%s, insert_date=%s "
diff --git a/backend/routers/users.py b/backend/routers/users.py
index 66d7c83b..2c8b0c8d 100644
--- a/backend/routers/users.py
+++ b/backend/routers/users.py
@@ -1,6 +1,7 @@
 from fastapi import APIRouter, HTTPException
 from pydantic import BaseModel
-from ..database import dbConnection
+#from ..database import dbConnection
+import database
 #SuperToken Auth from front end
 from supertokens_python.recipe.session.framework.fastapi import verify_session
 from supertokens_python.recipe.session import SessionContainer
@@ -25,7 +26,7 @@ class userUpdateRequest(BaseModel):
 #get user by email & doc Office ID
 @router.get("/users/profile/{email}", tags="users")
 async def read_all_users(email: str, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM users where email = %s"
     cursor.execute(query, (email.lower(),)) 
@@ -49,7 +50,7 @@ async def read_all_users(email: str, session: SessionContainer = Depends(verify_
 # Get List of all files
 @router.get("/users/", tags="users")
 async def read_all_users(session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM users"
     cursor.execute(query)
@@ -73,7 +74,7 @@ async def read_all_users(session: SessionContainer = Depends(verify_session())):
 # Get List of all files
 @router.get("/user/{uid}", tags="users")
 async def read_all_users(uid: str, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "SELECT * FROM users where app_id = %s"
     cursor.execute(query, (uid,))
@@ -97,7 +98,7 @@ async def read_all_users(uid: str, session: SessionContainer = Depends(verify_se
 # Insert Patient into table
 @router.post("/user/insert/", tags="user", status_code=201)
 async def insertPatient(itemRequest : userInsertRequest, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "insert into users "
     query += "(email, docOffice_id, fname, lname, type, app_id, username) "
@@ -117,7 +118,7 @@ async def insertPatient(itemRequest : userInsertRequest, session: SessionContain
 # Update User on table
 @router.put("/user/update/", tags="user")
 async def UpdateUser(itemRequest : userUpdateRequest, session: SessionContainer = Depends(verify_session())):
-    db = dbConnection.dbConnect()
+    db = database.dbConnection.dbConnect()
     cursor = db.cursor()
     query = "update users "
     query += "set username=%s, fname=%s, lname=%s "
diff --git a/docker-compose.yml b/docker-compose.yml
index 5c45efde..80747aae 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,13 +1,19 @@
 services:
 #============== API Hub ====================================================================
   api:
-    build: ./backend/
+    build:
+      context: ./backend
+      target: builder
     container_name: MIH-API-Hub
-    command: sh -c "sleep 10s; uvicorn backend.main:app --reload --port=8080 --host=0.0.0.0"
+    #command: sh -c "sleep 10s; uvicorn backend.main:app --reload --port=8080 --host=0.0.0.0"
+    #============Dev=================
+    # command: sh -c "sleep 10s; fastapi dev main.py --port 8080"
+    #============prod=================
+    #command: sh -c "sleep 10s; fastapi run backend/main.py --proxy-headers --port 8080"
     ports:
-      - 8080:8080
+      - 8080:80
     volumes:
-      - .:/app
+      - ./backend:/app
     networks:
       - MIH-network
     depends_on: