Make DESDEO2 runnable on Rahti

.s2i/bin/assemble

@@ -0,0 +1,98 @@
+#!/bin/bash
+
+function is_django_installed() {
+  python -c "import django" &>/dev/null
+}
+
+function should_collectstatic() {
+  is_django_installed && [[ -z "$DISABLE_COLLECTSTATIC" ]]
+}
+
+function virtualenv_bin() {
+    # New versions of Python (>3.6) should use venv module
+    # from stdlib instead of virtualenv package
+    python3.12 -m venv $1
+}
+
+# Install pipenv or micropipenv to the separate virtualenv to isolate it
+# from system Python packages and packages in the main
+# virtualenv. Executable is simlinked into ~/.local/bin
+# to be accessible. This approach is inspired by pipsi
+# (pip script installer).
+function install_tool() {
+  echo "---> Installing $1 packaging tool ..."
+  VENV_DIR=$HOME/.local/venvs/$1
+  virtualenv_bin "$VENV_DIR"
+  # First, try to install the tool without --isolated which means that if you
+  # have your own PyPI mirror, it will take it from there. If this try fails, try it
+  # again with --isolated which ignores external pip settings (env vars, config file)
+  # and installs the tool from PyPI (needs internet connetion).
+  # $1$2 combines package name with [extras] or version specifier if is defined as $2```
+  if ! $VENV_DIR/bin/pip install -U $1$2; then
+    echo "WARNING: Installation of $1 failed, trying again from official PyPI with pip --isolated install"
+    $VENV_DIR/bin/pip install --isolated -U $1$2  # Combines package name with [extras] or version specifier if is defined as $2```
+  fi
+  mkdir -p $HOME/.local/bin
+  ln -s $VENV_DIR/bin/$1 $HOME/.local/bin/$1
+}
+
+set -e
+
+# First of all, check that we don't have disallowed combination of ENVs
+if [[ ! -z "$ENABLE_PIPENV" && ! -z "$ENABLE_MICROPIPENV" ]]; then
+  echo "ERROR: Pipenv and micropipenv cannot be enabled at the same time!"
+  # podman/buildah does not relay this exit code but it will be fixed hopefuly
+  # https://github.com/containers/buildah/issues/2305
+  exit 3
+fi
+
+shopt -s dotglob
+echo "---> Installing application source ..."
+mv /tmp/src/* "$HOME"
+
+# set permissions for any installed artifacts
+fix-permissions /opt/app-root -P
+
+
+if [[ ! -z "$UPGRADE_PIP_TO_LATEST" ]]; then
+  echo "---> Upgrading pip, setuptools and wheel to latest version ..."
+  if ! pip install -U pip setuptools wheel; then
+    echo "WARNING: Installation of the latest pip, setuptools and wheel failed, trying again from official PyPI with pip --isolated install"
+    pip install --isolated -U pip setuptools wheel
+  fi
+fi
+
+pip install .[standard,api,server]
+
+
+if should_collectstatic; then
+  (
+    echo "---> Collecting Django static files ..."
+
+    APP_HOME=$(readlink -f "${APP_HOME:-.}")
+    # Change the working directory to APP_HOME
+    PYTHONPATH="$(pwd)${PYTHONPATH:+:$PYTHONPATH}"
+    cd "$APP_HOME"
+
+    # Look for 'manage.py' in the current directory
+    manage_file=./manage.py
+
+    if [[ ! -f "$manage_file" ]]; then
+      echo "WARNING: seems that you're using Django, but we could not find a 'manage.py' file."
+      echo "'manage.py collectstatic' ignored."
+      exit
+    fi
+
+    if ! python $manage_file collectstatic --dry-run --noinput &> /dev/null; then
+      echo "WARNING: could not run 'manage.py collectstatic'. To debug, run:"
+      echo "    $ python $manage_file collectstatic --noinput"
+      echo "Ignore this warning if you're not serving static files with Django."
+      exit
+    fi
+
+    python $manage_file collectstatic --noinput
+  )
+fi
+
+# set permissions for any installed artifacts
+fix-permissions /opt/app-root -P

.s2i/environment

@@ -0,0 +1,3 @@
+UPGRADE_PIP_TO_LATEST=1
+APP_MODULE=desdeo.api.app:app
+GUNICORN_CMD_ARGS=--bind=0.0.0.0:8080 --workers=2 --access-logfile=- --worker-class uvicorn.workers.UvicornWorker

desdeo/api/app.py

@@ -5,6 +5,7 @@
 from fastapi.middleware.cors import CORSMiddleware
 
 from desdeo.api.routers import NIMBUS, NAUTILUS_navigator, UserAuth, problems, test, NAUTILUS
+from desdeo.api.config import WebUIConfig
 
 app = FastAPI(
     title="DESDEO (fast)API",
@@ -19,7 +20,7 @@
 app.include_router(NAUTILUS_navigator.router)
 app.include_router(NAUTILUS.router)
 
-origins = ["http://localhost", "http://localhost:8080", "*"]
+origins = WebUIConfig.cors_origins
 
 app.add_middleware(
     CORSMiddleware,

desdeo/api/config.py

@@ -1,31 +1,38 @@
 """Configuration file."""
+import os
+import json
 
 from pydantic import (
     BaseModel,
     StrictStr,
     StrictInt,
     StrictBool
 )
-from typing import Optional, Union
+from typing import ClassVar, Optional, Union
 from datetime import timedelta
 
 class AuthConfig(BaseModel):
     """General configurations."""
 
     # openssl rand -hex 32
-    authjwt_secret_key: Optional[StrictStr] = "36b96a23d24cebdeadce6d98fa53356111e6f3e85b8144d7273dcba230b9eb18"
-    authjwt_algorithm: Optional[StrictStr] = "HS256"
-    authjwt_access_token_expires: Optional[StrictInt] = 15 # in minutes
-    authjwt_refresh_token_expires: Optional[StrictInt] = 30 # in minutes
+    authjwt_secret_key: ClassVar[StrictStr] = "36b96a23d24cebdeadce6d98fa53356111e6f3e85b8144d7273dcba230b9eb18"
+    authjwt_algorithm: ClassVar[StrictStr] = "HS256"
+    authjwt_access_token_expires: ClassVar[StrictInt] = 15 # in minutes
+    authjwt_refresh_token_expires: ClassVar[StrictInt] = 30 # in minutes
 
 class DBConfig(BaseModel):
     """Database configurations."""
 
-    db_host: Optional[StrictStr] = "localhost"
-    db_port: Optional[StrictStr] = "5432"
-    db_database: Optional[StrictStr] = "DESDEO3"
-    db_username: Optional[StrictStr] = "bhupindersaini"
-    db_password: Optional[StrictStr] = ""
-    db_pool_size: Optional[StrictInt] = 20
-    db_max_overflow: Optional[StrictInt] = 20
-    db_pool: Optional[StrictBool] = True
+    db_host: ClassVar[StrictStr] = os.getenv("POSTGRES_HOST") or "localhost"
+    db_port: ClassVar[StrictStr] = os.getenv("POSTGRES_PORT") or "5432"
+    db_database: ClassVar[StrictStr] = os.getenv("POSTGRES_DB") or "test"
+    db_username: ClassVar[StrictStr] = os.getenv("POSTGRES_USER") or "test"
+    db_password: ClassVar[StrictStr] = os.getenv("POSTGRES_PASSWORD") or "testpw"
+    db_pool_size: ClassVar[StrictInt] = int(os.getenv("POSTGRES_POOLSIZE") or 20)
+    db_max_overflow: ClassVar[StrictInt] = int(os.getenv("POSTGRES_OVERFLOW") or 20)
+    db_pool: ClassVar[StrictBool] = (os.getenv("POSTGRES_POOL") or True) in (True, 'true', '1', 't', 'y', 'yes')
+
+class WebUIConfig(BaseModel):
+    """Webui server configurations."""
+    # Below defaults to ["http://localhost", "http://localhost:8080"] if no env variable is set
+    cors_origins: ClassVar[list] = json.loads(os.getenv("CORS_ORIGINS",'["http://localhost", "http://localhost:8080"]'))

desdeo/api/db.py

@@ -9,12 +9,14 @@
 from sqlalchemy.orm import Session, sessionmaker
 from sqlalchemy_utils import create_database, database_exists, drop_database
 
+from desdeo.api.config import DBConfig
+
 # TODO: Extract this to a config file.
-DB_USER = "postgres"
-DB_PASSWORD = ""
-DB_HOST = "localhost"
-DB_PORT = "5432"
-DB_NAME = "DESDEO"
+DB_USER = DBConfig.db_username
+DB_PASSWORD = DBConfig.db_password
+DB_HOST = DBConfig.db_host
+DB_PORT = DBConfig.db_port
+DB_NAME = DBConfig.db_database
 
 
 SQLALCHEMY_DATABASE_URL = f"postgresql://{DB_USER}:{DB_PASSWORD}@{DB_HOST}:{DB_PORT}/{DB_NAME}"

desdeo/api/db_init.py

@@ -7,7 +7,7 @@
 from sqlalchemy_utils import create_database, database_exists, drop_database
 
 from desdeo.api import db_models
-from desdeo.api.db import SessionLocal, engine
+from desdeo.api.db import Base, SessionLocal, engine
 from desdeo.api.routers.UserAuth import get_password_hash
 from desdeo.api.schema import ObjectiveKind, ProblemKind, UserPrivileges, UserRole
 from desdeo.problem.schema import DiscreteRepresentation, Objective, Problem, Variable
@@ -23,13 +23,13 @@
 if not database_exists(engine.url):
     create_database(engine.url)
 else:
-    warnings.warn("Database already exists. Dropping and recreating it.", stacklevel=1)
-    drop_database(engine.url)
-    create_database(engine.url)
+    warnings.warn("Database already exists. Clearing it.", stacklevel=1)
+    # Drop all tables
+    Base.metadata.drop_all(bind=engine)
 print("Database tables created.")
 
 # Create the tables in the database.
-db_models.Base.metadata.create_all(bind=engine)
+Base.metadata.create_all(bind=engine)
 
 # Create test users
 db = SessionLocal()
@@ -61,7 +61,7 @@
     kind=ProblemKind.CONTINUOUS,
     obj_kind=ObjectiveKind.ANALYTICAL,
     value=problem.model_dump(mode="json"),
-    role_permission=[],
+    # role_permission=[],
 )
 
 db.add(problem_in_db)

pyproject.toml

@@ -32,6 +32,7 @@ pyomo = "^6.7.0"
 jupyter = "^1.0.0"
 jupyterlab = "^4.0.9"
 # API packages
+gunicorn = { version = "^23.0.0", optional = true }
 fastapi = { version = "^0.106.0", optional = true }
 uvicorn = { extras = ["standard"], version = "^0.25.0", optional = true }
 sqlalchemy = { version = "^2.0.23", optional = true }
@@ -59,6 +60,7 @@ api = [
     "python-jose",
     "bcrypt",
 ] # We could make API packages optional in the future.
+server = ["gunicorn"]
 
 [tool.poetry.group.dev.dependencies]
 ruff = "^0.3.0"