some rounding

.github/workflows/build-push-server.yaml

@@ -40,4 +40,4 @@ jobs:
           repository: dzdde/dzdmedlog
           short-description: "The server module for DZDMedLog, a system to document the medical history of study participant."
           enable-url-completion: true
-          readme-filepath: "README.md"
+          readme-filepath: "DOCKERHUB_README.md"

DOCKERHUB_README.md

@@ -0,0 +1,23 @@
+# DZDMedLog
+
+A Webapplication to log medication history of studyparticipants.
+
+For more details visit: https://github.com/DZD-eV-Diabetes-Research/DZDMedLog
+
+# Run
+
+## Prebuild container
+
+Get or Update the container image
+
+`docker pull dzdde/dzdmedlog`
+
+Run the container
+
+`docker run -v ./database:/opt/medlog/data -p 8888:8888 -e DEMO_MODE=true dzdde/dzdmedlog`
+
+(Alternatively) If you have a WiDo GKV Arzneimittelindex to hand:
+
+`docker run -v ./database:/opt/medlog/data ./GKV_AI_StammPlus:/opt/medlog/arzneimittelindex -p 8888:8888 -e DEMO_MODE=true dzdde/dzdmedlog`
+
+visit http://localhost:8888

Dockerfile

@@ -9,49 +9,57 @@ RUN bun install && bun run build && bunx nuxi generate
 
 # BACKEND BUILD AND RUN STAGE
 FROM python:3.11 AS medlog-backend
-RUN python3 -m pip install --upgrade pip
-COPY --from=medlog-frontend-build /frontend_build/.output/public /app 
-ENV DOCKER_MODE=1
-ENV FRONTEND_FILES_DIR=/app
-#RUN apt-get update && apt-get install git -y
-#
-ARG APPNAME=DZDMedLog
+ARG BASEDIR=/opt/medlog
 ARG MODULENAME=medlogserver
-#
+ENV MEDLOG_DOCKER_BASEDIR=$BASEDIR
+ENV DOCKER_MODE=1
+ENV FRONTEND_FILES_DIR=$BASEDIR/medlogfrontend
+
 # prep stuff
-RUN mkdir -p /opt/$APPNAME/$MODULENAME
-WORKDIR /opt/$APPNAME
+RUN mkdir -p $BASEDIR/medlogserver
+RUN mkdir -p $BASEDIR/medlogfrontend
+RUN mkdir -p $BASEDIR/data
+RUN mkdir -p $BASEDIR/provisioning/database
+RUN mkdir -p $BASEDIR/provisioning/arzneimittelindex
+
+# Copy frontend dist from pre stage
+COPY --from=medlog-frontend-build /frontend_build/.output/public $BASEDIR/medlogfrontend
+
+
+# Install Server
+WORKDIR $BASEDIR
+
+RUN python3 -m pip install --upgrade pip
 RUN pip install -U pip-tools
 
 # Generate requirements.txt based on depenencies defined in pyproject.toml
-COPY MedLog/backend/pyproject.toml /opt/$APPNAME/$MODULENAME
-RUN pip-compile -o /opt/$APPNAME/requirements.txt /opt/$APPNAME/$MODULENAME/pyproject.toml
+COPY MedLog/backend/pyproject.toml $BASEDIR/medlogserver/pyproject.toml
+RUN pip-compile -o $BASEDIR/requirements.txt $BASEDIR/medlogserver/pyproject.toml
 
 # Install requirements
-RUN pip install -U -r /opt/$APPNAME/requirements.txt
+RUN pip install -U -r $BASEDIR/requirements.txt
 
 # install app
-COPY MedLog/backend/medlogserver /opt/$APPNAME/$MODULENAME
+COPY MedLog/backend/medlogserver $BASEDIR/medlogserver
 
 # copy .git folder to be able to generate version file
-COPY .git /opt/$APPNAME/.git
-RUN echo "__version__ = '$(python -m setuptools_scm 2>/dev/null | tail -n 1)'" > /opt/$APPNAME/$MODULENAME/__version__.py
-# Remove git folder to reduce image size
-RUN rm -r /opt/$APPNAME/.git
+COPY .git $BASEDIR/.git
+RUN echo "__version__ = '$(python -m setuptools_scm 2>/dev/null | tail -n 1)'" > $BASEDIR/medlogserver/__version__.py
+# Remove git folder
+RUN rm -r $BASEDIR/.git
 
 #Copy default app data provisioning files
-RUN mkdir /prov
-COPY MedLog/backend/provisioning_data /provisioning
+COPY MedLog/backend/provisioning_data $BASEDIR/provisioning/database
+
 
 
-# Install data
-RUN mkdir -p /data/db
 # set base config
-WORKDIR /opt/$APPNAME/$MODULENAME
+WORKDIR $BASEDIR/medlogserver
 # set base config
 ENV SERVER_LISTENING_HOST=0.0.0.0
 ENV APP_PROVISIONING_DATA_YAML_FILES='[]'
-ENV DRUG_TABLE_PROVISIONING_SOURCE_DIR=/data/provisioning/arzneimittelindex
-ENV SQL_DATABASE_URL=sqlite+aiosqlite:////data/db/local.sqlite
+ENV DRUG_TABLE_PROVISIONING_SOURCE_DIR=$BASEDIR/provisioning/arzneimittelindex
+ENV SERVER_HOSTNAME=localhost
+ENV SQL_DATABASE_URL="sqlite+aiosqlite:///$BASEDIR/data/medlog.db"
 ENTRYPOINT ["python", "./main.py"]
 #CMD [ "python", "./main.py" ]

Makefile

@@ -0,0 +1,4 @@
+frontend:
+	./build_frontend.sh
+container:
+	./build_docker.sh

MedLog/backend/medlogserver/config.py

@@ -1,3 +1,5 @@
+from typing import List, Annotated, Optional, Literal, Dict
+from typing_extensions import Self
 from pydantic_settings import BaseSettings, SettingsConfigDict
 import os
 from pydantic import (
@@ -9,7 +11,7 @@
     StringConstraints,
     model_validator,
 )
-from typing import List, Annotated, Optional, Literal, Dict
+
 from pathlib import Path, PurePath
 import socket
 from textwrap import dedent
@@ -19,11 +21,13 @@
 
 
 class Config(BaseSettings):
-    APP_NAME: str = "DZD MedLog"
+    APP_NAME: str = "DZDMedLog"
     DOCKER_MODE: bool = False
     FRONTEND_FILES_DIR: str = Field(
         description="The generated nuxt dir that contains index.html,...",
-        default="MedLog/frontend/.output/public",
+        default=str(
+            Path(Path(__file__).parent.parent.parent, "frontend/.output/public")
+        ),
     )
     LOG_LEVEL: Literal["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"] = Field(
         default="INFO"
@@ -47,7 +51,8 @@ def demo_mode(self_data: dict):
                     self_data["APP_PROVISIONING_DATA_YAML_FILES"] = [
                         str(
                             Path(
-                                "/provisioning/demo_data/single_study_demo_data.yaml",
+                                os.getenv("MEDLOG_DOCKER_BASEDIR", "/opt/medlog"),
+                                "provisioning/database/demo_data/single_study_demo_data.yaml",
                             )
                         )
                     ]
@@ -103,8 +108,16 @@ def get_server_url(self) -> AnyHttpUrl:
         return AnyHttpUrl(f"{proto}://{self.SERVER_HOSTNAME}")
 
     CLIENT_URL: Optional[str] = Field(
-        default="http://localhost:5173", description="Origin url"
+        default=None,
+        description="The URL where the client is hosted. Usualy it comes with the server",
     )
+
+    @model_validator(mode="after")
+    def set_empty_client_url(self: Self):
+        if self.CLIENT_URL is None:
+            self.CLIENT_URL = self.get_server_url()
+        return self
+
     SQL_DATABASE_URL: AnyUrl = Field(default="sqlite+aiosqlite:///./local.sqlite")
 
     ADMIN_USER_NAME: str = Field(default="admin")
@@ -130,7 +143,7 @@ def get_server_url(self) -> AnyHttpUrl:
         description="Default data like some background jobs and vocabulary that is always loaded in the database. Under normal circustances this is nothing you need to changed. if you need to provision data like a Study into the database use the APP_PROVISIONING_DATA_YAML_FILES param.",
         default=str(Path(Path(__file__).parent, "default_data.yaml")),
     )
-
+    """Remove me on next refactor
     APP_CONFIG_PRESCRIBED_BY_DOC_ANSWERS: Dict = Field(
         default={
             "PRESCRIBED": "prescribed",
@@ -139,6 +152,7 @@ def get_server_url(self) -> AnyHttpUrl:
             "UNKNOWN": "unknown",
         }
     )
+    """
 
     APP_STUDY_PERMISSION_SYSTEM_DISABLED_BY_DEFAULT: bool = Field(
         default=False,

MedLog/backend/medlogserver/main.py

@@ -90,6 +90,15 @@ async def serve_frontend(path_name: Optional[str] = None):
             file = os.path.join(config.FRONTEND_FILES_DIR, "index.html")
         return FileResponse(file)
 
+    if config.CLIENT_URL == config.get_server_url():
+        if (
+            not Path(config.FRONTEND_FILES_DIR).exists()
+            or not Path(config.FRONTEND_FILES_DIR, "index.html").exists()
+        ):
+            raise ValueError(
+                "Can not find frontend files. Maybe you need to build the frontend first. Try to run 'make frontend'"
+            )
+
     uvicorn_log_config: Dict = LOGGING_CONFIG
     uvicorn_log_config["loggers"][APP_LOGGER_DEFAULT_NAME] = {
         "handlers": ["default"],
@@ -107,10 +116,29 @@ async def serve_frontend(path_name: Optional[str] = None):
     uvicorn_server = uvicorn.Server(config=uvicorn_config)
 
     event_loop.run_until_complete(init_db())
+    if config.DEMO_MODE:
+        log.info(
+            f"Hey, we are in demo mode. Login as admin with the following account:"
+        )
+        log.info(
+            f"USERNAME: {config.ADMIN_USER_NAME}\nPASSWORD: {config.ADMIN_USER_PW}"
+        )
     if with_background_worker:
         # Start background worker in second process
-        run_background_worker(run_in_extra_process=True)
-    event_loop.run_until_complete(uvicorn_server.serve())
+        background_worker = run_background_worker(run_in_extra_process=True)
+    try:
+        event_loop.run_until_complete(uvicorn_server.serve())
+    except (KeyboardInterrupt, Exception) as e:
+        if isinstance(e, KeyboardInterrupt):
+            log.info("KeyboardInterrupt shutdown...")
+        if isinstance(e, Exception):
+            log.info("Panic shutdown...")
+        if background_worker is not None:
+            log.info("Stop background worker process...")
+            background_worker.kill()
+            background_worker.join()
+        if isinstance(e, Exception):
+            raise e
 
 
 if __name__ == "__main__":

MedLog/backend/medlogserver/model/intake.py

@@ -28,9 +28,16 @@
 log = get_logger()
 config = Config()
 
-AdministeredByDoctorAnswers = enum.Enum(
-    "AdministeredByDoctorAnswers", config.APP_CONFIG_PRESCRIBED_BY_DOC_ANSWERS
-)
+# AdministeredByDoctorAnswers = enum.Enum(
+#    "AdministeredByDoctorAnswers", config.APP_CONFIG_PRESCRIBED_BY_DOC_ANSWERS
+# )
+
+
+class AdministeredByDoctorAnswers(str, enum.Enum):
+    PRESCRIBED = "prescribed"
+    RECOMMENDED = "recommended"
+    NO = "no"
+    UNKNOWN = "unknown"
 
 
 class IntakeRegularOrAsNeededAnswers(str, enum.Enum):

MedLog/backend/medlogserver/model/user.py

@@ -68,11 +68,11 @@ def validmail(cls, email):
         return email
 
     @model_validator(mode="after")
-    def val_display_name(self, values):
+    def val_display_name(self):
         """if no display name is set for now, we copy the identifying `user_name`"""
         if self.display_name is None:
             self.display_name = self.user_name
-        return values
+        return self
 
 
 class _UserWithName(UserBase, table=False):

MedLog/backend/medlogserver/model/user_auth.py

@@ -1,10 +1,11 @@
 # Basics
 from typing import AsyncGenerator, List, Optional, Literal, Sequence
+from typing_extensions import Self
 
 # Libs
 import enum
 import uuid
-from pydantic import SecretStr
+from pydantic import SecretStr, model_validator
 from sqlmodel import Field, Column, Enum, UniqueConstraint
 from passlib.context import CryptContext
 
@@ -45,7 +46,14 @@ class UserAuthUpdate(BaseTable, table=False):
 
 
 class UserAuthCreate(_UserAuthBase, UserAuthUpdate, table=False):
-    pass
+    @model_validator(mode="after")
+    def check_password_needed(self: Self):
+        if (
+            self.password is None
+            and self.auth_source_type == AllowedAuthSourceTypes.local
+        ):
+            raise ValueError("No empty password allowed for local users")
+        return self
 
 
 class UserAuth(_UserAuthBase, table=True):

MedLog/backend/medlogserver/worker/tasks/provisioning_data_loader.py

@@ -61,12 +61,12 @@ async def _parse_provisioning_file(self, path: Path):
                 file_content = yaml.safe_load(file_obj)
             except:
                 log.error(
-                    "Failed parsing provisioning data file at '{path}'. Data provisining will be canceled."
+                    "Failed parsing provisioning data file at '{path}'. Data provisioning will be canceled."
                 )
                 raise
         if not "items" in file_content:
             raise ValueError(
-                "Unexpected format in provisioning data file at '{path}'. Data provisining will be canceled."
+                "Unexpected format in provisioning data file at '{path}'. Data provisioning will be canceled."
             )
         if "items" in file_content and file_content["items"] is None:
             return

MedLog/backend/medlogserver/worker/worker.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Optional
 import asyncio
 import multiprocessing
 from apscheduler.schedulers.asyncio import AsyncIOScheduler
@@ -63,15 +63,17 @@ def _start_background_scheduler(event_loop=None):
 
 
 def run_background_worker(
-    run_in_extra_process: bool = True, event_loop: asyncio.AbstractEventLoop = None
-):
+    run_in_extra_process: bool = True,
+    event_loop: Optional[asyncio.AbstractEventLoop] = None,
+) -> Optional[multiprocessing.Process]:
     if run_in_extra_process:
         log.info("Start background worker in extra process...")
         background_worker_process = multiprocessing.Process(
             target=_start_background_scheduler, name="DZDMedLogBackgroundWorker"
         )
         background_worker_process.start()
         log.info(f"Started background worker (Process: {background_worker_process})")
+        return background_worker_process
     else:
         if event_loop is None:
             event_loop = asyncio.get_event_loop()