BioDiversityHub BC - updated

Sub-project under the SEISM Capital project, the source of BC’s species inventory data.

The objectives for the SIMS project are:

• To provide a single source for aquatic and terrestrial species and habitat data.
• To reduce the barriers for collecting and sharing aquatic and terrestrial species and habitat data throughout the province of British Columbia.
• To reduce the effort involved with managing aquatic and terrestrial species and habitat data.
• To improve access for all stakeholders to the aquatic and terrestrial species and habitat data needed to make informed decisions and policies for the province.

Pre-reqs

Install Node/NPM

• Requires Node version 12+
• https://nodejs.org/en/download/

Install Git

• https://git-scm.com/downloads

Clone the repo

• git clone https://github.com/bcgov/biohubbc.git

Install Docker

• https://www.docker.com/products/docker-desktop

Windows

Note: there are 2 mutually exclusive modes that Docker Desktop supports on Windows: Hyper-V or WSL2. You should be able to run the application in either mode, but this documentation was only written with instructions for Hyper-V. See https://code.visualstudio.com/blogs/2020/03/02/docker-in-wsl2 for possible instructions on using Docker Desktop in WSL2.

If prompted, install Docker using Hyper-V (not WSL 2)

Grant Docker access to your local folders

This setup uses volumes to support live reload.
Ensure Docker Desktop has access to your file system so that it can detect file changes and trigger live reload.

MacOS

• In the Docker-Desktop app:
  • Go to settings (gear icon)
  • Now go to Resources
  • Go to File Sharing
  • Add the folder/drive your repo is cloned under
    • This will grant Docker access to the files under it, which is necessary for it to detect file changes.

Windows

• In the Docker-Desktop app:
  • Go to settings (gear icon)
  • On the general tab ensure that the Use the WSL 2 based engine is unchecked.
    • If it is checked, uncheck it, and click Apply & Restart
      • Docker may crash, but that is fine, you can kill docker for now.
    • You will then need to go to the following URL and follow the instructions in the first section Enable Hyper-V using Powershell: https://docs.microsoft.com/en-us/virtualization/hyper-v-on-windows/quick-start/enable-hyper-v
      • This should just consist of running the 1 command in Powershell (as Admin): Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Hyper-V -All
    • Once the powershell command has been run, it will ask you to restart your machine.
    • Once restarted, re-launch Docker, and check that docker starts successfully and that the Use the WSL 2 based engine setting is still unchecked
  • Go to settings (gear icon)
  • Now go to Resources
  • Go to File Sharing
  • Add the folder/drive your repo is cloned under
    • This will grant Docker access to the files under it, which is necessary for it to detect file changes.

Ensure you can run the make command

MacOS

• Install make: brew install make
  • https://formulae.brew.sh/formula/make

Windows

• Install chocolatey: https://chocolatey.org/install#install-step2
• Install make: choco install make
  • https://community.chocolatey.org/packages/make

Note: you will need to run choco commands in a terminal as administrator

Configuring Local IDE

You can use any code IDE you prefer, though VSCode is recommended.

• https://code.visualstudio.com/

For convenience, you can install all node_modules by running the following command from the repo's root folder.

make install

You can also manually run npm install in each of the /api/, /app/, and /database/ folders.

Building/Running the App

Note: Run all make commands from the root folder of the repo.

Note: Run all commands in a terminal that supports make. On Mac you can use the default Terminal, on Windows you can use git-bash.

Initialize the ./env file.

This will copy ./env_config/env.docker to ./.env.
This should only need to be run once.
This file may need additional editing to provide secrets for external services (like S3).

make env

Result of running make env for the first time:

Start all Applications

Starts all applications (database, api, app).

make web

Result of running make web (condensed to only show the important parts):

Access the Running Applications

api:

• localhost:6100/api/

app:

• localhost:7100

Helpful Makefile Commands

See ./Makefile for all available commands.

Note: Run all make commands from the root folder of the repo.

Print Makefile Help Doc

make help

Install All Dependencies

Will run npm install in each of the project folders (api, app, database).

make install

Delete All Containers

Will stop and delete the application docker containers.
This is useful when you want to clear out all database content, returning it to its initial default state.
After you've run make clean, running make web will launch new containers, with a fresh instance of the database.

make clean

View the logs for a container

API

make log-api

APP

make log-app

Database

make log-db

Database Setup (migrations + seeding)

make log-db-setup

Run Linter and Fix Issues

Will run the projects code linter and attempt to fix all issues found.

Note: Not all formatting issues can be auto-fixed.

make lint-fix

Run Formatter and Fix Issues

Will run the projects code formatter and attempt to fix all issues found.

Note: Not all formatting issues can be auto-fixed.

make format-fix

Shell Into a Docker Container (database, api, app, etc)

See ./Makefile for all available commands.

Database

This is useful if you want to access the PSQL database through the CLI.
See DBeaver for a GUI-centric way of accessing the PSQL database.

make db-container

Helpful Docker Commands

Show all running containers

docker ps

Show all containers (running and closed)

docker ps -a

What a successfully built/run set of docker containers looks like:

Note: The exited container is correct, as that container executes database migrations and then closes

View the logs for a container

docker logs <container id or name>
Include -f to "follow" the container logs, showing logs in real time

Prune Docker Artifacts

Over a long period time, Docker can run out of storage memory. When this happens, docker will log a message indicating it is out of memory.

The below command will delete docker artifacts to recover docker hard-drive space.

See documentation for OPTIONS.

docker system prune [OPTIONS]

Troubleshooting

Make Issues

If you get an error saying the make command is not found, you may need to install it first.
See Ensure you can run the make command

Docker Service Issues

ENV

A docker service can fail if required environment variables can't be found.
Double check that your .env has the latest variables from env.docker, which may have been updated.

Docker Timezone Issue

While trying to run a make command such as make web, if you encounter an issue along the lines of:

E: Release file for http://deb.debian.org/debian/dists/buster-updates/InRelease is not valid yet (invalid for another 1d 1h 5min 13s). Updates for this repository will not be applied.

it may be possible that your system clock is out of date or not synced (dockerfile timezone has to match your machine timezone). In this case, make sure your timezone is correct and matches that of docker and restart your machine/terminal window and try again.

Database Container Wont Start

If you already had PostgreSQL (PSQL) installed, it is likely that the default port 5432 is already in use and the instance running in Docker fails because it can't acquire that port.

• You can either stop the existing PSQL service, freeing up the port for Dockers use.
• Or alter the DB_PORT environment variable in .env to something not in use (ex: 5433).
  • You will likely need to run make clean and make web to ensure the containers are re-built with the new variables.

The App Works Locally But Not In OpenShift

Ensure that any new environment variables have been included in all of the necessary files.

Local Development

• env.docker
• docker-compose.yml
• app/src/contexts/configContext.tsx

Deployed to OpenShift

• [api/app/database]/.pipeline/**
• server/index.js
• app/src/contexts/configContext.tsx
• OpenShift Secrets [dev,test,prod]

Helpful Tools

DBeaver

GUI-centric application for viewing/interacting with Databases.

• https://dbeaver.io/

Pre-req

• Intall PostgreSQL 12+
• https://www.postgresql.org/download/

Add a new connection

• Click New Database Connection (+ icon)
  • Host: localhost
  • Port: 5432
  • Database: biohubbc
  • username: postgres
  • password: postgres
  • user role: (leave empty)
  • local client: PostgreSQL 12

Note: all of the above connection values can be found in the .env file

Acknowledgements

License

Copyright 2019 Province of British Columbia

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.