Merge branch 'server-deployment' into 'master'

Server deployment

See merge request !14

.gitignore

 .idea
 config/
+venv/
 p.py
 __pycache__
 /hypercorn.access
 /hypercorn.error
 .pyc
+server.md
\ No newline at end of file

.gitlab-ci.yml

-# This file is a template, and might need editing before it works on your project.
-# To contribute improvements to CI/CD templates, please follow the Development guide at:
-# https://docs.gitlab.com/ee/development/cicd/templates.html
-# This specific template is located at:
-# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Python.gitlab-ci.yml
-
-# Official language image. Look for the different tagged releases at:
-# https://hub.docker.com/r/library/python/tags/
-image: python:latest
-
 # Change pip's cache directory to be inside the project directory since we can
 # only cache local items.
 variables:
@@ -23,8 +13,14 @@ cache:
     - .cache/pip
     - venv/
 
+stages:
+  - build
+  - test
+  - deploy
+
 build-job:
   stage: build
+  image: python:latest
   script:
     - python -V
     - pip install virtualenv
@@ -38,24 +34,65 @@ build-job:
 
 test-job1:
   stage: test
+  image: python:latest
   script:
     - source venv/bin/activate
     - flake8 --config .flake8
 
 test-job2:
   stage: test
+  image: python:latest
   script:
     - source venv/bin/activate
     - mypy --config-file=pyproject.toml server
 
-
-#pages:
-#  script:
-#    - pip install sphinx sphinx-rtd-theme
-#    - cd doc ; make html
-#    - mv build/html/ ../public/
-#  artifacts:
-#    paths:
-#      - public
-#  rules:
-#    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+deploy-to-production:
+  stage: deploy
+  tags:
+    - bare-metal
+  script:
+    - echo "Current working directory and user"
+    - pwd
+    - whoami
+    - groups
+    - echo $HOME
+    - echo "Reset git config"
+    - rm /home/gitlab-runner/.gitconfig
+    - git config --global url."https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pik-potsdam.de/".insteadOf "ssh://git@gitlab.pik-potsdam.de/"
+    - git config --global user.name gitlab-runner
+    - git config --global user.email gitlab-runner@gitlab.pik-potsdam.de
+    - git config --global -l --show-origin
+    - echo "Go to deployment location"
+    - cd /home/nacsos/nacsos-core
+    - ls -lisah
+    - sudo chown -R gitlab-runner /home/nacsos/nacsos-core
+    - sudo chgrp -R gitlab-runner /home/nacsos/nacsos-core
+    - ls -lisah
+    - echo "Stopping NACSOS-core service"
+    - sudo systemctl stop nacsos-core.service
+    - echo "Dropping virtual environment"
+    - rm -rf venv
+    - echo "Fetching updated source"
+    - git stash  # "reset" softly by stashing (in case files changed)
+    - git pull origin production  # pull from origin (production branch)
+    - echo "Creating new virtual environment"
+    - python3.10 -m venv venv
+    - source venv/bin/activate
+    - echo "Installing requirements"
+    - pip install -r requirements.txt
+    - echo "Handling migrations"
+    - pip install alembic
+    - cd /home/nacsos/nacsos-core/venv/src/nacsos-data/
+    - alembic upgrade head
+    - sudo chown -R nacsos /home/nacsos/nacsos-core
+    - sudo chgrp -R nacsos /home/nacsos/nacsos-core
+    - echo "Starting NACSOS-core service"
+    - sudo systemctl start nacsos-core.service
+# DEPRECATED
+#    - echo "Run as nacsos user"
+#    - sudo -u nacsos bash ./deploy.sh $CI_JOB_TOKEN
+#    - echo "Becoming 'nacsos' user"
+#    - sudo -u nacsos -s
+  when: manual
+  only:
+    - production

README.md

@@ -3,6 +3,10 @@ This repository contains the core data management platform of NACSOS.
 It accesses the database via the `nacsos-data` package and exposes the functionality via an API.
 It also serves the web frontend.
 
+```
+pg_dump -d nacsos_core -h localhost -U root -W -p 5432 > dump.sql
+```
+ 
 ## Installation
 - Requires Python 3.10+, tested with Python 3.10.2
 

requirements.txt

@@ -9,4 +9,4 @@ httpx[http2]==0.23.1
 pymitter==0.4.0
 uvicorn==0.20.0
 python-multipart==0.0.5
--e git+ssh://git@gitlab.pik-potsdam.de/mcc-apsis/nacsos/nacsos-data.git@d98b527cada27517332d195028d9bacea93844f5#egg=nacsos_data
+-e git+ssh://git@gitlab.pik-potsdam.de/mcc-apsis/nacsos/nacsos-data.git@e9713a94c7a50484c9a204c5514cfdea7d962694#egg=nacsos_data

server/__init__.py

@@ -17,7 +17,7 @@ mimetypes.init()
 
 logger = get_logger('nacsos.server')
 
-app = FastAPI()
+app = FastAPI(openapi_url=settings.SERVER.OPENAPI_FILE)
 
 logger.debug('Setting up server and middlewares')
 mimetypes.add_type('application/javascript', '.js')
@@ -43,5 +43,5 @@ app.mount('/', StaticFiles(directory=settings.SERVER.STATIC_FILES, html=True), n
 
 
 @app.on_event("startup")
-def on_startup():
-    db_engine.startup()
+async def on_startup():
+    await db_engine.startup()

server/api/routes/annotations.py

 from pydantic import BaseModel
 from sqlalchemy import select
 from sqlalchemy.orm import load_only
-from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.ext.asyncio import AsyncSession  # noqa: F401
 from fastapi import APIRouter, Depends, HTTPException, status as http_status, Query
 
 from nacsos_data.db.schemas import \

server/util/config.py

@@ -20,6 +20,7 @@ class ServerConfig(BaseModel):
     DEBUG_MODE: bool = False  # set this to true in order to get more detailed logs
     WORKERS: int = 2  # number of worker processes
     STATIC_FILES: str = '../nacsos-web/dist/'  # path to the static files to be served
+    OPENAPI_FILE: str = '/openapi.json'  # absolute URL path to openapi.json file
 
     HASH_ALGORITHM: str = 'HS256'
     SECRET_KEY: str = secrets.token_urlsafe(32)