Refactor/dockercompose+docs by ALION999 · Pull Request #112 · datasci4citizens/server-wounds

ALION999 · 2026-02-17T19:17:24Z

inicio do refactor da parte da API e documentação (modifiquei apenas o readme por enquanto), models usados da versão anterior. google auth implementado.

Copilot

Pull request overview

This PR starts a major refactor/migration of the server codebase from the legacy FastAPI/SQLModel implementation to a Django + Django REST Framework API, along with updates to documentation, Docker templates, and inclusion of OMOP-related models/utilities.

Changes:

Added/updated Django project skeleton (citizens_project/) and DRF authentication endpoints (Google login + JWT).
Removed large portions of the legacy FastAPI/SQLModel server code and related docs/docker artifacts under old/src / old/docs / old/docker.
Added/updated assorted documentation and ML/data scripts under docs/ and old/ (OMOP mappings, model scripts, dataset utilities).

Reviewed changes

Copilot reviewed 80 out of 141 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
requirements.txt	New dependency list for Django-based stack (currently malformed encoding).
.gitignore	Simplified ignore rules (now risks committing env/secret files).
.env.model	Updated env template for DB + Google credentials (formatting issues).
.dockerignore	Updated Docker build ignore list.
docker/dockerfile	Dockerfile updated for Django runserver.
docker/docker-compose-model.yml	New docker-compose template for Postgres + Django web.
citizens_project/citizens_project/settings.py	Django settings updated for Postgres + DRF + Google OAuth.
citizens_project/citizens_project/urls.py	Project URL routing updated (API mounted under `/api/`).
citizens_project/citizens_project/asgi.py	Django ASGI config doc link/version update.
citizens_project/citizens_project/wsgi.py	Django WSGI config doc link/version update.
citizens_project/app_cicatrizando/api.py	DRF ViewSets for `auth/login/google` and `auth/me`.
citizens_project/app_cicatrizando/urls.py	DRF router wiring + Swagger UI route.
citizens_project/app_cicatrizando/serializers.py	Serializers adjusted to `fields='__all__'`.
citizens_project/app_cicatrizando/apps.py	AppConfig simplified.
citizens_project/app_cicatrizando/google.py	Minor formatting change (Google helper module).
citizens_project/app_cicatrizando/views.py	Replaced prior viewsets with placeholder view module.
citizens_project/app_cicatrizando/tests.py	Added placeholder Django test module.
citizens_project/app_cicatrizando/omop/omop_models.py	Minor whitespace cleanup.
citizens_project/app_cicatrizando/omop/omop_serializers.py	Minor formatting cleanup.
citizens_project/app_cicatrizando/omop/omop_ids.py	Minor formatting cleanup.
citizens_project/app_cicatrizando/admin.py	Removed prior admin registrations; placeholder remains.
docs/Readme.md	New Portuguese setup/run documentation.
docs/Descricao1.txt	Minor formatting update.
docs/model.md	Placeholder (empty).
docs/mapeamento_conceptID/cid.py	Cleanup of inline markers/typos in mapping constants/comments.
docs/mapeamento_conceptID/wound_type.txt	Minor formatting cleanup.
docs/mapeamento_conceptID/smoke_frequency.txt	Formatting fix for closing brace indentation.
docs/mapeamento_conceptID/Descricao1.txt	Added mapping documentation draft.
docs/mapeamento_conceptID/Descricao2.txt	Added extended OMOP mapping description draft.
docs/mapeamento_conceptID/Descricao3.txt	Added additional mapping/notes draft.
docs/identification_model/*	Added model training/inference utilities + README + gitignore.
docs/infection_ischemia_model/*	Added multi-label training/inference utilities + gitignore.
old/requirements.txt	Replaced legacy dependency set with Django-focused set (contains duplicates).
old/README.md	Updated legacy README content to Django-based instructions.
old/Dockerfile	Updated legacy Dockerfile from FastAPI to Django runserver.
old/.gitignore	Added ignore rules in `old/` subtree.
old/.env.model	Updated legacy env template fields.
old/filter_concepts.py	Added one-off CSV filtering script.
old/src/** (multiple)	Removed legacy FastAPI/SQLModel implementation modules (auth/db/api/schema/utils).
old/docs/** (multiple)	Removed legacy FastAPI/SQLModel/Postgres docs.
old/docker/** (multiple)	Removed legacy docker compose templates and MinIO Dockerfile.
old/migrations/** (multiple)	Removed Alembic migration scaffolding.
README.md	Deleted root README (docs moved under `docs/` and `old/`).
docker-compose.yml	Removed old root-level compose file.
docker/dbms/docker-compose-modelo.yml	Removed older DB-only compose template.

Comments suppressed due to low confidence (1)

docker/dockerfile:2

Using an unpinned base image (FROM python) can cause non-reproducible builds and sudden breakages when the default tag updates. Pin to a specific major/minor (and ideally a slim variant) that matches the project's supported runtime.

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Copilot · 2026-02-17T19:28:34Z

citizens_project/app_cicatrizando/urls.py

 urlpatterns = [
    path('', include(router.urls)),
-    path('', include(virtual_urls.router.urls)),
-    path("api/schema/", SpectacularAPIView.as_view(), name="schema"),
-    path("docs/redoc", SpectacularRedocView.as_view(), name="redoc"),
-    path("docs/swagger", SpectacularSwaggerView.as_view(), name="schema-swagger-ui"),
-    path("docs", scalar_viewer, name="schema-scalar-ui"), 
-] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+
+    path('docs/', SpectacularSwaggerView.as_view(url_name='schema'), name='swagger-ui'),
+]


SpectacularSwaggerView.as_view(url_name='schema') will raise NoReverseMatch because there is no URL pattern named schema registered (no SpectacularAPIView route is defined). Add a schema endpoint (and name it schema) or update url_name to match the actual schema route.

Copilot · 2026-02-17T19:28:35Z

citizens_project/citizens_project/urls.py

 urlpatterns = [
-    path('api-auth/', include('rest_framework.urls', namespace='rest_framework')),
-    path('', include('app_cicatrizando.urls')),
    path('admin/', admin.site.urls),


This module imports SpectacularAPIView / SpectacularSwaggerView but does not register a schema route. Since app_cicatrizando/urls.py references url_name='schema', the project URLconf should expose a SpectacularAPIView path named schema (typically under /api/schema/) or remove the unused imports and adjust the docs route accordingly.

Suggested change

path('admin/', admin.site.urls),

path('admin/', admin.site.urls),

path('api/schema/', SpectacularAPIView.as_view(), name='schema'),

path('api/docs/', SpectacularSwaggerView.as_view(url_name='schema'), name='api-docs'),

Copilot · 2026-02-17T19:28:35Z

citizens_project/app_cicatrizando/api.py

        logger.debug("Google login request")
        auth_serializer = self.serializer_class(data=request.data)
-        auth_serializer.is_valid(raise_exception=True) # Valida os dados da requisição.
+        auth_serializer.is_valid(raise_exception=True)
        validated_data = auth_serializer.validated_data
        logger.debug(f"Validated data: {validated_data}")
-        # Obtém os dados do usuário do Google.
+
+        # Obtém os dados do usuário do Google
        user_data = google_get_user_data(validated_data)
        logger.debug(f"User data from Google: {user_data}")


These debug logs include validated_data (OAuth code / ID token) and user_data (PII such as email/name). This can leak sensitive data into logs. Remove these logs or redact sensitive fields before logging (and prefer structured logging with explicit safe fields).

Copilot · 2026-02-17T19:28:36Z

citizens_project/citizens_project/settings.py

+REST_FRAMEWORK = {
+    'DEFAULT_AUTHENTICATION_CLASSES': [
+        'rest_framework_simplejwt.authentication.JWTAuthentication',
    ],


REST_FRAMEWORK sets authentication but not default permissions, so endpoints without an explicit permission_classes will default to AllowAny. If the intended default is authenticated access (as in the prior code), set DEFAULT_PERMISSION_CLASSES to IsAuthenticated and override only the login endpoints.

Suggested change

],

],

'DEFAULT_PERMISSION_CLASSES': [

'rest_framework.permissions.IsAuthenticated',

],

Copilot · 2026-02-17T19:28:36Z

.env.model

+SERVER_WOUNDS_DB_HOST=db #
 SERVER_WOUNDS_DB_PORT=5432
-SERVER_WOUNDS_SECRET_KEY="chave"
-SERVER_WOUNDS_DISABLE_AUTH=false
+
+SERVER_WOUNDS_SECRET_KEY= your-secret-key-here #
+GOOGLE_CLIENT_ID= your-client-id #
+GOOGLE_CLIENT_SECRET= your-client-secret #


This env template includes leading spaces after = and inline # markers, which many dotenv parsers treat as part of the value (or can be confusing). Remove the leading spaces and move comments to separate lines so copy/paste produces a valid .env.

Copilot · 2026-02-17T19:28:36Z

docker/docker-compose-model.yml

+    depends_on:
+      db:
+        condition: service_healthy
+    restart: on-failure:3


depends_on: condition: service_healthy requires the db service to define a healthcheck. As written, docker compose will error because db has no healthcheck. Add a Postgres healthcheck (e.g., pg_isready) or change the dependency condition to service_started.

Copilot · 2026-02-17T19:28:36Z

citizens_project/citizens_project/settings.py

 # SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY =  os.environ["SERVER_WOUNDS_SECRET_KEY"]
-GOOGLE_OAUTH2_CLIENT_ID = os.environ["GOOGLE_CLIENT_ID"]
-GOOGLE_OAUTH2_CLIENT_SECRET = os.environ["GOOGLE_CLIENT_SECRET"]
-DISABLE_AUTH = "true" == os.environ.get("SERVER_WOUNDS_DISABLE_AUTH", "false")
+SECRET_KEY = os.environ.get("SERVER_WOUNDS_SECRET_KEY", "django-insecure-changeme")
+
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True

-ALLOWED_HOSTS = [
-    'server.wounds.paas.ic.unicamp.br',
-    'server.wounds.staging.paas.ic.unicamp.br',
-    'localhost',
-    '127.0.0.1'
-]
+ALLOWED_HOSTS = []



SECRET_KEY falls back to a hardcoded insecure default, and ALLOWED_HOSTS is always empty (even though docker-compose provides ALLOWED_HOSTS). This makes it easy to misdeploy with an unsafe key and can break requests when DEBUG is off. Prefer reading ALLOWED_HOSTS from env (comma-separated) and require SERVER_WOUNDS_SECRET_KEY when DEBUG is false.

ALION999 added 3 commits February 16, 2026 16:27

remade docker compose, docs, and readded google auth

2aa5782

docs/readme updated

84796cf

small fix on documentation

db60ea5

Copilot AI review requested due to automatic review settings February 17, 2026 19:17

Copilot started reviewing on behalf of ALION999 February 17, 2026 19:18 View session

Copilot AI reviewed Feb 17, 2026

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Refactor/dockercompose+docs#112

Refactor/dockercompose+docs#112
ALION999 wants to merge 3 commits intomainfrom
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-    ],
+    ],
+    'DEFAULT_PERMISSION_CLASSES': [
+        'rest_framework.permissions.IsAuthenticated',
+    ],

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