From c74e058e75eacd3bf46fa8e5a6f54f0a3f8c2341 Mon Sep 17 00:00:00 2001
From: David Wilby <d.wilby@sheffield.ac.uk>
Date: Thu, 30 Sep 2021 18:22:01 +0100
Subject: [PATCH] add postgres db for staging and production

---
 annotation_tool/settings/production.py |  16 ++-
 annotation_tool/settings/staging.py    |  13 +-
 create-django-db.sh                    |  10 ++
 db-migrate.sh                          |   7 +
 docker-compose.yml                     |  45 ++++---
 environment.yml                        | 175 +++++++++++++++++++++++--
 6 files changed, 231 insertions(+), 35 deletions(-)
 create mode 100755 create-django-db.sh
 create mode 100755 db-migrate.sh

diff --git a/annotation_tool/settings/production.py b/annotation_tool/settings/production.py
index 497c96c6..4609d345 100644
--- a/annotation_tool/settings/production.py
+++ b/annotation_tool/settings/production.py
@@ -1,5 +1,9 @@
+<<<<<<< HEAD
 import logging
 import sys
+=======
+import os
+>>>>>>> add postgres db for staging and production
 from .base import *
 
 # Enable csrf in production
@@ -33,4 +37,14 @@
            'propagate': True,
        },
    },
-}
\ No newline at end of file
+}
+DATABASES = {
+    'default': {
+        'ENGINE': 'django.db.backends.postgresql',
+        'NAME': os.environ.get("DJANGO_DB_NAME", "annotations_db"),
+        "USER": os.environ.get("DB_USERNAME", "user"),
+        "PASSWORD": os.environ.get("DB_PASSWORD", "password"),
+        "HOST": os.environ.get("DB_HOST", "db"),
+        "PORT": os.environ.get("DB_PORT", "5432"),
+    }
+}
diff --git a/annotation_tool/settings/staging.py b/annotation_tool/settings/staging.py
index fd12fd10..2c88a493 100644
--- a/annotation_tool/settings/staging.py
+++ b/annotation_tool/settings/staging.py
@@ -1,3 +1,4 @@
+import os
 from .base import *
 
 # Enable csrf in production
@@ -30,4 +31,14 @@
            'propagate': True,
        },
    },
-}
\ No newline at end of file
+}
+DATABASES = {
+    'default': {
+        'ENGINE': 'django.db.backends.postgresql',
+        'NAME': os.environ.get("DJANGO_DB_NAME", "annotations_db"),
+        "USER": os.environ.get("DB_USERNAME", "user"),
+        "PASSWORD": os.environ.get("DB_PASSWORD", "password"),
+        "HOST": os.environ.get("DB_HOST", "db"),
+        "PORT": os.environ.get("DB_PORT", "5432"),
+    }
+}
diff --git a/create-django-db.sh b/create-django-db.sh
new file mode 100755
index 00000000..cc844252
--- /dev/null
+++ b/create-django-db.sh
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<EOSQL
+CREATE USER $DJANGO_DB_USER WITH PASSWORD '$DJANGO_DB_PASSWORD';
+CREATE DATABASE $DJANGO_DB_NAME;
+GRANT ALL PRIVILEGES ON DATABASE $DJANGO_DB_NAME TO $DJANGO_DB_USER;
+CREATE USER $DB_BACKUP_USER WITH PASSWORD '$DB_BACKUP_PASSWORD';
+GRANT CONNECT ON DATABASE $DJANGO_DB_NAME TO $DB_BACKUP_USER;
+GRANT USAGE ON SCHEMA public TO $DB_BACKUP_USER;
+EOSQL
diff --git a/db-migrate.sh b/db-migrate.sh
new file mode 100755
index 00000000..96a0d87e
--- /dev/null
+++ b/db-migrate.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+#
+# Run Django migrations against the postgresql container to create the initial
+# schema or migrate after an upgrade
+#
+
+docker-compose run --rm --entrypoint "python" backend manage.py migrate
\ No newline at end of file
diff --git a/docker-compose.yml b/docker-compose.yml
index d55c04c9..528c6aa7 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -14,10 +14,9 @@ services:
       - DJANGO_DB_NAME
       - DB_USERNAME
       - DB_PASSWORD
-    # depends_on:
-    #   - db
+    depends_on:
+      - db
     volumes:
-      - ./db.sqlite3:/app/db.sqlite3
       - logs/:/logs/
     networks:
       - django-nginx
@@ -31,33 +30,33 @@ services:
       - 80:80
     depends_on:
       - backend
-      # - db
+      - db
     networks:
       - django-nginx
 
 
-#   db:
-#     image: postgres:12-alpine
-#     restart: always
-#     expose:
-#       - "5432"
-#     env_file: 
-#       - ./.env
-#     environment:
-#       - POSTGRES_USER=postgres
-#       - POSTGRES_PASSWORD=${PG_SUPERUSER_PASSWORD}
-#       - DJANGO_DB_NAME
-#       - DJANGO_DB_USER=${DB_USERNAME}
-#       - DJANGO_DB_PASSWORD=${DB_PASSWORD}
-#       - DB_BACKUP_USER
-#       - DB_BACKUP_PASSWORD
-#     volumes:
-#       - postgresql-data:/var/lib/postgresql/data
-#       - ./create-django-db.sh:/docker-entrypoint-initdb.d/001-create-django-db.sh
+  db:
+    image: postgres:12-alpine
+    restart: always
+    expose:
+      - "5432"
+    env_file: 
+      - ./.env
+    environment:
+      - POSTGRES_USER=postgres
+      - POSTGRES_PASSWORD=${PG_SUPERUSER_PASSWORD}
+      - DJANGO_DB_NAME
+      - DJANGO_DB_USER=${DB_USERNAME}
+      - DJANGO_DB_PASSWORD=${DB_PASSWORD}
+      - DB_BACKUP_USER
+      - DB_BACKUP_PASSWORD
+    volumes:
+      - postgresql-data:/var/lib/postgresql/data
+      - ./create-django-db.sh:/docker-entrypoint-initdb.d/001-create-django-db.sh
 
 volumes:
   logs:
-#   postgresql-data:
+  postgresql-data:
 
 networks:
   django-nginx:
diff --git a/environment.yml b/environment.yml
index 806c5e88..90f7ee4e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,15 +1,15 @@
 name: annotation-tool
 channels:
-  - conda-forge
-  - https://repo.anaconda.com/pkgs/free
   - anaconda
+  - https://repo.anaconda.com/pkgs/free
+  - conda-forge
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=main
   - brotlipy=0.7.0=py39h27cfd23_1003
-  - ca-certificates=2021.4.13=h06a4308_1
+  - ca-certificates=2021.7.5=h06a4308_1
   - cairo=1.14.8=0
-  - certifi=2020.12.5=py39h06a4308_0
+  - certifi=2021.5.30=py39h06a4308_0
   - cffi=1.14.5=py39h261ae71_0
   - chardet=4.0.0=py39h06a4308_1003
   - conda=4.10.1=py39hf3d152e_0
@@ -22,6 +22,7 @@ dependencies:
   - freetype=2.5.5=2
   - glib=2.50.2=1
   - graphviz=2.38.0=5
+  - gunicorn=20.1.0=py39h06a4308_0
   - harfbuzz=0.9.39=2
   - icu=68.1=h58526e2_0
   - idna=2.10=pyhd3eb1b0_0
@@ -42,12 +43,13 @@ dependencies:
   - ncurses=6.2=he6710b0_1
   - networkx=2.5.1=pyhd3eb1b0_0
   - nodejs=12.19.0=hfa01f41_2
-  - openssl=1.1.1k=h27cfd23_0
+  - openssl=1.1.1l=h7f8727e_0
   - pango=1.40.3=1
   - pcre=8.39=1
   - pip=21.0.1=py39h06a4308_0
   - pixman=0.34.0=hceecf20_3
   - postgresql=12.2=h20c2e04_0
+  - psycopg2=2.8.6=py39h3c74f83_1
   - pycosat=0.6.3=py39h27cfd23_0
   - pycparser=2.20=py_2
   - pyopenssl=20.0.1=pyhd3eb1b0_1
@@ -69,25 +71,178 @@ dependencies:
   - yaml=0.2.5=h7b6447c_0
   - zlib=1.2.11=h7b6447c_3
   - pip:
+    - aiohttp==3.7.4.post0
+    - aiohttp-cors==0.7.0
+    - alabaster==0.7.12
+    - anyio==3.0.1
+    - apipkg==1.5
+    - appdirs==1.4.4
+    - argon2-cffi==20.1.0
     - asgiref==3.3.2
+    - astroid==2.4.1
+    - async-generator==1.10
+    - async-timeout==3.0.1
     - attrs==20.3.0
+    - babel==2.9.1
+    - backcall==0.2.0
+    - bandit==1.7.0
+    - beautifulsoup4==4.9.3
+    - black==21.5b1
+    - bleach==3.3.0
+    - blis==0.7.4
+    - catalogue==2.0.4
+    - click==7.1.2
+    - conllu==4.4
+    - coverage==5.5
+    - cymem==2.0.5
+    - defusedxml==0.7.1
+    - distlib==0.3.1
     - django==3.2
     - django-extensions==3.1.3
+    - django-webpack-loader==0.7.0
     - djangorestframework==3.12.4
+    - docutils==0.16
+    - dodgy==0.2.1
+    - entrypoints==0.3
+    - execnet==1.8.0
+    - filelock==3.0.12
+    - flake8==3.8.4
+    - flake8-polyfill==1.0.2
+    - frosted==1.4.1
+    - gatenlp==1.0.4
+    - gitdb==4.0.7
+    - gitpython==3.1.17
+    - imagesize==1.2.0
     - iniconfig==1.1.1
+    - install==1.3.4
+    - ipykernel==5.5.5
+    - ipython==7.23.1
+    - ipython-genutils==0.2.0
+    - ipywidgets==7.6.3
+    - isort==4.3.21
+    - jedi==0.18.0
+    - jinja2==3.0.0
+    - joblib==1.0.1
+    - json5==0.9.5
+    - jsonschema==3.2.0
+    - jupyter-client==6.1.12
+    - jupyter-core==4.7.1
+    - jupyter-server==1.7.0
+    - jupyterlab==3.0.15
+    - jupyterlab-pygments==0.1.2
+    - jupyterlab-server==2.5.1
+    - jupyterlab-widgets==1.0.0
+    - lazy-object-proxy==1.4.3
+    - mako==1.1.4
+    - markdown==3.3.4
+    - markupsafe==2.0.0
+    - matchtext==0.2.3
+    - matplotlib-inline==0.1.2
+    - mccabe==0.6.1
+    - mistune==0.8.4
+    - msgpack==1.0.2
+    - multidict==5.1.0
+    - murmurhash==1.0.5
+    - mypy==0.812
+    - mypy-extensions==0.4.3
+    - nbclassic==0.2.8
+    - nbclient==0.5.3
+    - nbconvert==6.0.7
+    - nbformat==5.1.3
+    - nest-asyncio==1.5.1
+    - nltk==3.6.2
+    - notebook==6.3.0
+    - numpy==1.20.3
     - packaging==20.9
+    - pandocfilters==1.4.3
+    - parso==0.8.2
+    - pathspec==0.8.1
+    - pathy==0.5.2
+    - pbr==5.6.0
+    - pdoc3==0.9.2
+    - pep8==1.7.1
+    - pep8-naming==0.10.0
+    - pexpect==4.8.0
+    - pickleshare==0.7.5
+    - pies==2.6.7
     - pluggy==0.13.1
+    - preshed==3.0.5
+    - prometheus-client==0.10.1
+    - prompt-toolkit==3.0.18
+    - prospector==1.3.1
+    - protobuf==3.17.0
+    - ptyprocess==0.7.0
     - py==1.10.0
+    - py4j==0.10.9.2
+    - pycodestyle==2.6.0
+    - pydantic==1.7.4
+    - pydocstyle==6.0.0
     - pydot==1.4.2
+    - pyflakes==2.2.0
+    - pygments==2.9.0
     - pygraphviz==1.7
+    - pylint==2.5.3
+    - pylint-celery==0.3
+    - pylint-django==2.1.0
+    - pylint-flask==0.6
+    - pylint-plugin-utils==0.6
     - pyparsing==2.4.7
+    - pyroma==3.1
+    - pyrsistent==0.17.3
     - pytest==6.2.3
+    - pytest-cache==1.0
+    - pytest-cov==2.12.0
     - pytest-django==4.2.0
+    - pytest-pep8==1.0.6
+    - pytest-runner==5.3.0
+    - pytest-tornasync==0.6.0.post2
+    - python-dateutil==2.8.1
     - pytz==2021.1
+    - pyyaml==5.4.1
+    - pyzmq==22.0.3
+    - recordclass==0.14.3
+    - regex==2021.4.4
+    - requirements-detector==0.7
+    - rise==5.7.1
+    - send2trash==1.5.0
+    - setoptconf==0.2.0
+    - smart-open==3.0.0
+    - smmap==4.0.0
+    - sniffio==1.2.0
+    - snowballstemmer==2.1.0
+    - sortedcontainers==2.3.0
+    - soupsieve==2.2.1
+    - spacy==3.0.6
+    - spacy-legacy==3.0.5
+    - sphinx==3.5.4
+    - sphinxcontrib-applehelp==1.0.2
+    - sphinxcontrib-devhelp==1.0.2
+    - sphinxcontrib-htmlhelp==1.0.3
+    - sphinxcontrib-jsmath==1.0.1
+    - sphinxcontrib-qthelp==1.0.3
+    - sphinxcontrib-serializinghtml==1.1.4
     - sqlparse==0.4.1
+    - srsly==2.4.1
+    - stanza==1.2
+    - stevedore==3.3.0
+    - terminado==0.9.5
+    - testpath==0.4.4
+    - thinc==8.0.3
     - toml==0.10.2
-    - gatenlp
-    - pyyaml
-    - msgpack
-    - bs4
-prefix: /home/twin/miniconda3/envs/annotation-tool
+    - torch==1.8.1
+    - tornado==6.1
+    - tox==3.23.1
+    - traitlets==5.0.5
+    - typed-ast==1.4.3
+    - typer==0.3.2
+    - typing-extensions==3.10.0.0
+    - virtualenv==20.4.6
+    - voila==0.2.10
+    - vulture==2.3
+    - wasabi==0.8.2
+    - wcwidth==0.2.5
+    - webencodings==0.5.1
+    - websocket-client==0.59.0
+    - widgetsnbextension==3.5.1
+    - wrapt==1.12.1
+    - yarl==1.6.3