start server via docker

.gitignore

@@ -14,3 +14,5 @@
 .cache
 __pycache__
 *.pyc
+
+/app-dev.cfg

Dockerfile

@@ -26,7 +26,7 @@ ARG install_dev
 COPY requirements.dev.txt ./
 RUN if [ "${install_dev}" = "y" ]; then pip install -r requirements.dev.txt; fi
 
-COPY --from=client --chown=elife:elife /home/node/client/ ${PROJECT_FOLDER}/client/
+COPY --from=client --chown=elife:elife /home/node/client/dist/ ${PROJECT_FOLDER}/client/dist/
 COPY --chown=elife:elife peerscout/ ${PROJECT_FOLDER}/peerscout/
 COPY --chown=elife:elife server.sh ${PROJECT_FOLDER}/
 COPY --chown=elife:elife update-data-and-reload.sh ${PROJECT_FOLDER}/
@@ -35,7 +35,7 @@ COPY --chown=elife:elife app-defaults.cfg ${PROJECT_FOLDER}/
 
 USER root
 RUN mkdir .data && chown www-data:www-data .data
-RUN mkdir logs && chown www-data:www-data logs
+RUN mkdir logs && chown www-data:www-data logs && chmod -R a+w logs
 
 USER www-data
-CMD ["venv/bin/python"]
+CMD ["/srv/peerscout/server.sh"]

Dockerfile.client

@@ -10,3 +10,5 @@ COPY --chown=node:node client/package.json client/package-lock.json ./
 RUN npm ci
 
 COPY --chown=node:node client ./
+
+RUN npm run bundle

Makefile

@@ -3,7 +3,7 @@ DOCKER_COMPOSE_CI = docker-compose -f docker-compose.yml
 DOCKER_COMPOSE = $(DOCKER_COMPOSE_DEV)
 
 
-.PHONY: all test clean build
+.PHONY: all test clean build logs
 
 
 dev-venv:
@@ -31,7 +31,11 @@ client-shell: client-build
 
 
 server-build:
-	$(DOCKER_COMPOSE) build peerscout
+	# only dev compose file has "init" service defined
+	@if [ "$(DOCKER_COMPOSE)" = "$(DOCKER_COMPOSE_DEV)" ]; then \
+		$(DOCKER_COMPOSE) build init; \
+	fi
+	$(DOCKER_COMPOSE) build client peerscout
 
 
 server-build-dev:
@@ -42,12 +46,64 @@ server-test: server-build-dev
 	$(DOCKER_COMPOSE) run --rm peerscout-dev ./project_tests.sh
 
 
-server-shell: server-build
+server-dev-shell: server-build-dev
+	$(DOCKER_COMPOSE) run --rm peerscout-dev bash
+
+
+db-start:
+	$(DOCKER_COMPOSE) up -d db
+
+
+migrate-schema: server-build
+	$(DOCKER_COMPOSE) run --rm --user elife peerscout ./migrate-schema.sh
+
+
+update-data-and-reload: server-build
+	$(DOCKER_COMPOSE) run --rm --user elife peerscout ./update-data-and-reload.sh
+
+
+fix-data-permissions:
+	mkdir -p .data
+	chmod -R a+w .data
+
+
+start: server-build
+	$(DOCKER_COMPOSE) up -d peerscout
+
+
+stop:
+	$(DOCKER_COMPOSE) stop peerscout
+
+
+www-shell:
+	$(DOCKER_COMPOSE) exec peerscout bash
+
+
+www-shell-run:
 	$(DOCKER_COMPOSE) run --rm peerscout bash
 
 
-server-dev-shell: server-build-dev
-	$(DOCKER_COMPOSE) run --rm peerscout-dev bash
+elife-shell:
+	$(DOCKER_COMPOSE) exec --user elife peerscout bash
+
+
+elife-shell-run:
+	$(DOCKER_COMPOSE) run --rm --user elife peerscout bash
+
+
+restart: stop start
+
+
+down:
+	$(DOCKER_COMPOSE) down
+
+
+clean:
+	$(DOCKER_COMPOSE) down -v
+
+
+logs:
+	$(DOCKER_COMPOSE) logs -f
 
 
 build: .PHONY

README.md

@@ -1,16 +1,79 @@
-# Pre-requisites
+# PeerScout
+
+## Configuration
+
+### AWS Credentials and Configuration
+
+Create `~/.aws/credentials` and populate the credentials, e.g.:
+
+```ini
+[default]
+aws_access_key_id=<key id>
+aws_secret_access_key=<access key>
+```
+
+You may also create `~/.aws/config`:
+
+```ini
+[default]
+region=<region>
+```
+
+### App Configuration
+
+Copy `app-example.cfg` to `app.cfg` and make the necessary configuration changes.
+
+When using Docker for development, the configuration file is `app-dev.cfg` instead.
+It would very much have the same config but the database should point to the `db` service (defined in [docker-compose.override.yml](docker-compose.override.yml)).
+
+## Development with Docker
+
+### Pre-requisites (with Docker)
+
+* [Docker](https://www.docker.com/) and [Docker Compose](https://docs.docker.com/compose/)
+
+### Create / Migrate Schema (with Docker)
+
+```bash
+make migrate-schema
+```
+
+### Populate Database (with Docker)
+
+This will download updates from AWS and populate the database with it. This may take a while. It will also download data from Crossref, which might fail, which is 'okay'.
+
+```bash
+make update-data-and-reload
+```
+
+### Data Directory
+
+Downloaded files and cache are stored to the `.data` directory. Which in development is mounted to the host. To make the directory writable by the Docker user (`elife`) call (writable to all users):
+
+```bash
+make fix-data-permissions
+```
+
+### Start
+
+```bash
+make start
+```
+
+## Development without Docker
+
+### Pre-requisites (without Docker)
 
 * Python 3 (including dev dependencies, e.g. `python3-dev` on Ubunutu / Debian)
 * system dev dependencies (e.g. `build-essential`)
 * [PostgreSQL](https://www.postgresql.org/) (although [SQLite](https://sqlite.org/) may work too)
 * [Node.js](https://nodejs.org/) and [npm](https://www.npmjs.com/)
 
+### Setup (without Docker)
 
-# Setup
+#### Python Dependencies
 
-## Python Dependencies
-
-### A) Using Local Virtual Environment
+##### A) Using Local Virtual Environment
 
 If you want to use a separate virtual environment (`venv`) for this project.
 
@@ -19,7 +82,7 @@ If you want to use a separate virtual environment (`venv`) for this project.
 source venv/bin/activate
 ```
 
-### B) Using Your Own Virtual Environment
+##### B) Using Your Own Virtual Environment
 
 Assuming you already created and switched to your own virtual environment.
 
@@ -33,7 +96,7 @@ Download SpaCy models (~1 GB).
 python -m spacy.en.download all
 ```
 
-## Database
+#### Database
 
 The recommended database is [PostgreSQL](https://www.postgresql.org/).
 
@@ -46,50 +109,29 @@ sudo -u postgres psql -c "alter user reviewer_suggestions_user with encrypted pa
 sudo -u postgres psql -c "grant all privileges on database reviewer_suggestions_db to reviewer_suggestions_user;"
 ```
 
-## AWS Credentials and Configuration
-
-Create `~/.aws/credentials` and populate the credentials, e.g.:
-
-```ini
-[default]
-aws_access_key_id=<key id>
-aws_secret_access_key=<access key>
-```
-
-You may also create `~/.aws/config`:
-
-```ini
-[default]
-region=<region>
-```
-
-## App Configuration
-
-Copy `app-example.cfg` to `app.cfg` and make the necessary configuration changes.
-
-## Create / Update Database Schema
+#### Create / Update Database Schema
 
 ```bash
 python -m peerscout.preprocessing.migrateSchema
 ```
 
-## Populate Database
+#### Populate Database
 
 This will download updates from AWS and populate the database with it. This may take a while. It will also download data from Crossref, which might fail, which is 'okay'.
 
 ```bash
 python -m peerscout.preprocessing.updateDataAndReload
 ```
 
-## Compile Client
+#### Compile Client
 
 ```bash
 cd client
 npm install
 npm run bundle
 ```
 
-# Start Server
+### Start Server
 
 ```bash
 python -m peerscout.server
@@ -99,7 +141,7 @@ Then go to [http://localhost:8080/](http://localhost:8080/). (If you are getting
 
 The server will provide the REST API [http://localhost:8080/api/](http://localhost:8080/api/) and serve the static client bundle.
 
-# Start Client Dev Server
+### Start Client Dev Server
 
 Use this option to develop the client, in addition to the python server (which will still provide the API).
 
@@ -110,15 +152,15 @@ npm start
 
 Then server will be availabe under [http://localhost:8081/](http://localhost:8081/).
 
-# Tests
+### Tests
 
-## Run All Tests
+#### Run All Tests
 
 ```bash
 ./project_tests.sh
 ```
 
-## Python Tests
+#### Python Tests
 
 ```bash
 pytest

docker-compose.override.yml

@@ -0,0 +1,41 @@
+version: '3'
+
+services:
+  init:
+    build:
+      context: ./docker/init
+      dockerfile: Dockerfile
+    image: elifesciences/peerscout_init:${IMAGE_TAG}
+    volumes:
+      - config-aws:/home/elife/volume-config-aws
+      - ~/.aws:/home/elife/user-config-aws
+
+  db:
+    image: postgres:9.6
+    restart: always
+    volumes:
+      - postgres-data:/var/lib/postgresql/data
+    environment:
+      POSTGRES_DB: peerscout_db
+      POSTGRES_USER: peerscout_user
+      POSTGRES_PASSWORD: peerscout_password
+    healthcheck:
+      test: ["CMD", "bash", "-c", "echo > /dev/tcp/localhost/5432"]
+      interval: 10s
+      timeout: 10s
+      retries: 5
+    ports:
+      - "9432:5432"
+
+  peerscout:
+    depends_on:
+      - client
+      - db
+      - init
+    volumes:
+      - ./app-dev.cfg:/srv/peerscout/app.cfg
+      - ./.data:/srv/peerscout/.data
+      - config-aws:/home/elife/.aws
+
+volumes:
+  config-aws:

docker-compose.yml

@@ -15,9 +15,10 @@ services:
       args: 
         commit: ${IMAGE_TAG}
     image: elifesciences/peerscout:${IMAGE_TAG}
-    command: /bin/sh -c exit 0
     depends_on:
       - client
+    ports:
+      - "8080:8080"
 
   peerscout-base-dev:
     build:
@@ -41,3 +42,6 @@ services:
     command: /bin/sh -c exit 0
     depends_on:
       - peerscout-base-dev
+
+volumes:
+  postgres-data:

docker/init/Dockerfile

@@ -0,0 +1,5 @@
+FROM busybox:1.30.1
+
+COPY init.sh /bin/
+
+CMD /bin/init.sh

docker/init/init.sh

@@ -0,0 +1,14 @@
+#!/bin/sh
+
+set -e
+
+# elife user id
+USER_ID=1000
+echo 'changing ownership to $USER_ID, and...'
+
+echo 'copying aws credentials...'
+
+cp -r /home/elife/user-config-aws/* /home/elife/volume-config-aws
+chown -R $USER_ID:$USER_ID /home/elife/volume-config-aws
+
+echo 'done'