Merge pull request #46 from janash/upgrade/backend

upgrade backend image and pydantic version

backend/app/app/core/config.py

@@ -1,4 +1,5 @@
-from pydantic import BaseSettings, PostgresDsn, validator
+from pydantic import PostgresDsn, validator
+from pydantic_settings import SettingsConfigDict, BaseSettings
 
 from typing import Any, Optional, Dict
 
@@ -12,20 +13,20 @@ class Settings(BaseSettings):
     POSTGRES_DB: str
     SQLALCHEMY_DATABASE_URI: Optional[PostgresDsn] = None
 
+    # TODO[pydantic]: We couldn't refactor the `validator`, please replace it by `field_validator` manually.
+    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-validators for more information.
     @validator("SQLALCHEMY_DATABASE_URI", pre=True)
     def assemble_db_connection(cls, v: Optional[str], values: Dict[str, Any]) -> Any:
         if isinstance(v, str):
             return v
         return PostgresDsn.build(
             scheme="postgresql",
-            user=values.get("POSTGRES_USER"),
+            username=values.get("POSTGRES_USER"),
             password=values.get("POSTGRES_PASSWD"),
             host=values.get("POSTGRES_SERVER"),
-            path=f"/{values.get('POSTGRES_DB') or ''}"
+            path=f"{values.get('POSTGRES_DB') or ''}"
         )
-
-    class Config:
-        case_sensitive = True
+    model_config = SettingsConfigDict(case_sensitive=True)
 
 
 settings = Settings()

backend/app/app/db/session.py

@@ -10,7 +10,7 @@ class Models:
 
 
 Base = automap_base()
-engine = create_engine(settings.SQLALCHEMY_DATABASE_URI, pool_pre_ping=True)
+engine = create_engine(str(settings.SQLALCHEMY_DATABASE_URI), pool_pre_ping=True)
 SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
 Base.prepare(engine, reflect=True)
 

backend/app/app/schemas/molecule.py

@@ -6,29 +6,29 @@
 class Molecule(BaseModel):
     molecule_id: int
     smiles: str
-    molecular_weight: Optional[float]
+    molecular_weight: Optional[float] = None
     conformers_id: List[Optional[int]]
-    dft_data: Optional[Dict]
-    xtb_data: Optional[Dict]
-    xtb_ni_data: Optional[Dict]
-    ml_data: Optional[Dict]
+    dft_data: Optional[Dict] = None
+    xtb_data: Optional[Dict] = None
+    xtb_ni_data: Optional[Dict] = None
+    ml_data: Optional[Dict] = None
 
 class MoleculeSimple(BaseModel):
     molecule_id: int
-    umap1: Optional[float]
-    umap2: Optional[float]
-    pat: Optional[str]
+    umap1: Optional[float] = None
+    umap2: Optional[float] = None
+    pat: Optional[str] = None
     smiles: str
 
 class MoleculeComponents(BaseModel):
-    type: Optional[str]
+    type: Optional[str] = None
     molecule_id: int
-    pat: Optional[str]
+    pat: Optional[str] = None
     smiles: str
-    components: Optional[list[float]]
+    components: Optional[list[float]] = None
 
 class MoleculeNeighbors(MoleculeComponents):
-    dist: Optional[float]
+    dist: Optional[float] = None
 
 class MoleculeIdentifiers(BaseModel):
     smiles: str

backend/app/prestart.sh

@@ -1,11 +1,11 @@
-#!/bin/sh
+#!/bin/bash
 
-# Wait for DB to be ready
-$python $(pwd)/app/backend_prestart.py
+# Initialize the shell for micromamba
+eval "$(micromamba shell hook --shell bash)"
 
-# Upgrade if needed
-#alembic upgrade head
+# Activate the environment. If you're using a different environment name other than "base", replace it.
+micromamba activate base
 
-# Start FastAPI
+# Navigate to app directory and start FastAPI using Uvicorn.
 cd app
 uvicorn main:app --reload --port 8080 --host 0.0.0.0

backend/backend.dockerfile

@@ -1,8 +1,12 @@
-FROM continuumio/miniconda3
+FROM mambaorg/micromamba
 
-RUN yes | conda install -c conda-forge rdkit fastapi alembic psycopg2-binary "sqlalchemy<2.0" tenacity uvicorn curl openbabel
+COPY environment.yaml* /tmp/conda-tmp/
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+RUN micromamba install -f /tmp/conda-tmp/environment.yaml && \
+    micromamba clean --all --yes
 
 WORKDIR /app/
 ADD ./app /app/
-RUN pip install -e .
-
+RUN pip install -e .

backend/environment.yaml

@@ -0,0 +1,16 @@
+name: base
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python
+  - rdkit
+  - fastapi
+  - pydantic-settings
+  - alembic 
+  - psycopg2-binary 
+  - sqlalchemy 
+  - tenacity 
+  - uvicorn 
+  - curl 
+  - openbabel