Merge pull request #20 from fenfisdi/issue/9/insert_cmodels_in_database

Issue/9/insert cmodels in database

This PR was initially opened to address issue #9. However The issue was indirectly related to these other issues that will also be closed. 

closes #9
closes #23
closes #10
closes #21

.gitignore

@@ -151,3 +151,6 @@ cython_debug/
 
 # Experiments
 experiments/
+
+# MacOS
+.DS_Store

Dockerfile

@@ -0,0 +1,20 @@
+FROM python:3.8-slim-buster
+EXPOSE 8080
+
+ENV PYTHONUNBUFFERED 1
+ENV APP_HOME /app
+
+COPY requirements.txt .
+
+RUN pip install --no-cache-dir -U pip \
+    && pip install --no-cache-dir -r requirements.txt
+
+WORKDIR ${APP_HOME}
+
+COPY src src
+COPY main.py .
+COPY docker-entrypoint.sh .
+COPY .env .
+
+ENTRYPOINT ["/bin/bash"]
+CMD ["./docker-entrypoint.sh"]

docker-compose.yml

@@ -0,0 +1,32 @@
+version: "3.5"
+services:
+  user_app:
+    build: .
+    container_name: cdslab_models_app
+    env_file: .env
+    image: cdslab_user
+    networks:
+      - cdslab_models
+    ports:
+      - 5000:5000
+    volumes:
+    - ./src:/app/src
+
+  user_mongo:
+    container_name: cdslab_models_mongo
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: cdsuser
+      MONGO_INITDB_ROOT_PASSWORD: cdspass
+    image: mongo:3-xenial
+    networks:
+      - cdslab_models
+    ports:
+      - 27017:27017
+    volumes:
+      - /tmp/data/cdslab_models/:/data/db
+
+
+networks:
+  cdslab_models:
+    name: cdslab_user
+    driver: bridge

docker-entrypoint.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+if [ -z "${PORT}" ] ; then PORT=8080; fi
+
+if [ -z "${HOST}" ] ; then HOST=0.0.0.0; fi
+
+uvicorn main:app --port=${PORT} --host=${HOST} --reload

main.py

@@ -1,11 +1,18 @@
+from src.db.mongo import MongoClientSingleton
 import uvicorn
+
+from src.api import app
 from src.config import settings
+from src.use_cases.cmodels import CmodelUseCases
 
-if __name__ == '__main__':
+__all__ = ['app']
 
+if __name__ == '__main__':
+    mongo_singleton = MongoClientSingleton()
+    CmodelUseCases(mongo_singleton).update_cmodels_collection()
     uvicorn.run(
         "src.api:app",
-        host=settings['HOST'],
+        host=settings.get('HOST'),
         port=int(settings['PORT']),
         reload=True,
         debug=True,

requirements.txt

@@ -23,6 +23,7 @@ iniconfig==1.1.1
 mccabe==0.6.1
 mongomock==3.22.1
 packaging==20.9; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pandas==1.2.4
 pluggy==0.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 py==1.10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pycodestyle==2.7.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
@@ -33,6 +34,7 @@ pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3
 pytest-cov==2.11.1
 pytest==6.2.3
 python-dotenv==0.17.0
+python-multipart==0.0.5
 requests==2.25.1
 sentinels==1.0.0
 six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'

src/api.py

@@ -7,18 +7,17 @@
 
 app = FastAPI()
 
-
 app.add_middleware(
     TrustedHostMiddleware,
-    allowed_hosts=settings["ALLOWED_HOSTS"].split(",")
+    allowed_hosts=settings.get("ALLOWED_HOSTS", "*").split(",")
 )
 
 app.add_middleware(
     CORSMiddleware,
     allow_credentials=True,
-    allow_origins=settings["ALLOWED_ORIGINS"].split(","),
-    allow_methods=settings["ALLOWED_METHODS"].split(","),
-    allow_headers=settings["ALLOWED_HEADERS"].split(",")
+    allow_origins=settings.get("ALLOWED_ORIGINS", "*").split(","),
+    allow_methods=settings.get("ALLOWED_METHODS", "*").split(","),
+    allow_headers=settings.get("ALLOWED_HEADERS", "*").split(",")
 )
 
 app.include_router(

src/config.py

@@ -1,5 +1,5 @@
 from dotenv import dotenv_values
 
 
-settings = dotenv_values(".env")
-db_config = dotenv_values(".db_config")
+settings = dotenv_values('.env')
+db_config = dotenv_values('.db_config')

src/db/mongo.py

@@ -1,47 +1,87 @@
-from typing import Generator, Tuple
+from typing import Generator, Optional, Tuple, Union
+
 from pymongo import MongoClient
+from pymongo.collection import Collection
 from pymongo.database import Database
+import mongomock
 
 from src.config import db_config
+from src.utils.patterns import Singleton
+
+
+class MongoClientSingleton(metaclass=Singleton):
+    db_uri: Optional[str] = db_config.get('MONGO_URI'),
+
+    def __init__(
+        self,
+        db_connection: MongoClient = MongoClient(db_uri),
+        db: Union[str, Database] = db_config.get('MONGO_DB'),
+        coll: Union[str, Collection] = db_config.get('CMODELS_COLL')
+    ) -> None:
+        self.db_connection = db_connection
+        self.db = db
+        self.coll = coll
+
+    def api_get_db_connection(self) -> Generator[MongoClient, None, None]:
+        """Creates connection to Mongodb server.
+
+        Yields
+        ------
+        db_connection: MongoClient
+            Object containing the db connection.
+        """
+        try:
+            yield self.db_connection
+        finally:
+            self.db_connection.close()
+
+    def get_db(
+        self,
+        db: Optional[str] = None
+    ) -> Tuple[MongoClient, Database]:
+        """Gets Mongodb connection and database.
+
+        Returns
+        -------
+        db_connection : MongoClient
+        db : pymongo.database.Database
+        """
+        if db and isinstance(db, str):
+            self.db = db
+        return self.db_connection, self.db
+
+    def get_collection(
+        self,
+        coll: Optional[str] = None
+    ) -> Tuple[MongoClient, Collection]:
+        """
+        Returns
+        -------
+        db_connection: pymongo.MongoClient
+        coll: pymongo.collection.Collection
+        """
+        if coll and isinstance(coll, str):
+            self.coll = coll
+        return self.db_connection, self.coll
+
+    @property
+    def db(self):
+        return self._db
+
+    @db.setter
+    def db(self, value):                                                 # noqa
+        if isinstance(value, str):
+            self._db = self.db_connection[value]
+        elif isinstance(value, Database) or isinstance(value, mongomock.Database):
+            self._db = value
 
+    @property
+    def coll(self):
+        return self._coll
 
-def api_get_db_connection(
-    db_uri: str = db_config['MONGO_URI'],
-) -> Generator[MongoClient, None, None]:
-    """Creates connection to Mongodb server.
-
-    Yields
-    ------
-    db_connection: MongoClient
-        Object containing the db connection.
-    """
-    db_connection = MongoClient(db_uri)
-
-    try:
-        yield db_connection
-    finally:
-        db_connection.close()
-
-
-def get_db(
-    db_uri: str = db_config['MONGO_URI'],
-    db_name: str = db_config['MONGO_DB']
-) -> Tuple[MongoClient, Database]:
-    """Gets Mongodb connection and database.
-
-    Parameters
-    ----------
-    db_uri: str
-        Mongo server URI.
-    db_name: str
-        Mongo database name.
-
-    Returns
-    -------
-    db_connection : MongoClient
-    db : pymongo.database.Database
-    """
-    db_connection = MongoClient(db_uri)
-    db: Database = db_connection[db_name]
-
-    return db_connection, db
+    @coll.setter
+    def coll(self, value):                                               # noqa 
+        if isinstance(value, str):
+            self._coll = self.db[value]
+        elif isinstance(value, Collection) or isinstance(value, mongomock.Collection):
+            self._coll = value

src/interfaces/cmodels.py

@@ -0,0 +1,60 @@
+from datetime import datetime
+
+from src.db.mongo import MongoClientSingleton
+from src.models.db.cmodels import (
+    CompartmentalModel,
+    CompartmentalModelEnum
+)
+from src.interfaces.crud import MongoCRUD
+
+
+class CModelsInterface:
+
+    def __init__(
+        self,
+        mongo_singleton: MongoClientSingleton
+    ) -> None:
+        self.mongo_singleton = mongo_singleton
+        self.crud = MongoCRUD(self.mongo_singleton)
+
+    def insert_one_cmodel_document(self, model: CompartmentalModel):
+
+        cmodel_document = model.dict(by_alias=True)
+
+        existent_model = self.crud.read(model.id)
+
+        if existent_model:
+            pruned_existent_model = CModelsInterface._prune_db_document(
+                existent_model
+            )
+            pruned_current_model = CModelsInterface._prune_db_document(
+                cmodel_document
+            )
+            if pruned_existent_model == pruned_current_model:
+                # TODO: log cmodel exists f'Cmodel exists: {model.name}'
+                return existent_model
+            else:
+                model.updated_at = datetime.utcnow()
+                updated_model = self.crud.update(
+                    model.id,
+                    model.dict(by_alias=True)
+                )
+                # TODO log updated cmodel f'Updated cmodel: {model.name}'
+                return updated_model
+        else:
+            model_inserted = self.crud.insert(cmodel_document)
+            # TODO: log created cmodel f'Created cmodel: {model.name}'
+            return model_inserted
+
+    def insert_all_cmodel_documents(self):
+        return [
+            self.insert_one_cmodel_document(model)
+            for model in CompartmentalModelEnum.values()
+        ]
+
+    @staticmethod
+    def _prune_db_document(model_in_db: dict) -> dict:
+        if model_in_db:
+            model_in_db.pop('inserted_at')
+            model_in_db.pop('updated_at')
+            return model_in_db