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Macbook setup
These instructions describe software installations for MacOS as of 6/24/2021 and are based on an Intel-based Mac running Big Sur (macOS v11.4). Any problems with this process may result from a different architecture, OS version, or newer versions of the software being installed.
Note: MacOS uses Z shell (zsh) as the default shell. If you prefer bash, you can make that the default shell under System Preferences > Users and Groups (unlock the lock icon to make changes) > right click your user, select 'Advanced Options' and change 'Login shell' to /bin/bash. Alternatively, you can set your default shell to bash using chsh -s /bin/bash. If using bash add export BASH_SILENCE_DEPRECATION_WARNING=1 to ~/.bashrc or ~/.bash_profile and continue to update that same file instead of ~/.zshrc throughout this setup.
- Slack
- Zoom
- OneDrive*
- Web browser, such as Chrome*
- LastPass browser extension
- Text editor, such as VSCode
- AWS CLI v2
- Postgres.app (get "Postgres.app with all currently supported versions" - we are currently running v10.x in production)
- pgAdmin4
* may already be installed by UW IT
Follow the Homebrew installation instructions here.
At time of writing, MacOS ships with Python 2.7.16 (/usr/bin/python) and Python 3.8.2 (/usr/bin/python3). We will leave these installed but will not use them, instead opting for pyenv to manage python versions (starting with Python 3.6.9 to match current production server).
brew install zlib sqlite bzip2 libiconv libzip xz pyenv
LDFLAGS="-L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib" CPPFLAGS="-I$(brew --prefix xz)/include" pyenv install --patch 3.6.9 < <(curl -sSL https://github.com/python/cpython/commit/8ea6353.patch\?full_index\=1)
Add the following line to ~/.zshrc:
export PATH=/Users/<your system username>/.pyenv/versions/3.6.9/bin:$PATH
Then restart terminal. Now python --version and python3 --version should show version 3.6.9.
Next install pipenv and envdir:
pip install pipenv envdir
Production system was upgraded to Python 3.9.10 on 2/8/2022. To install Python 3.9.10 using pyenv, and make it your default version:
pyenv install 3.9.10
Add the following (or replace existing) line in ~/.zshrc:
export PATH=/Users/<your system username>/.pyenv/versions/3.9.10/bin:$PATH
Then restart terminal. Now python --version and python3 --version should show version 3.9.10.
Next install pipenv and envdir:
pip install pipenv envdir
At time of writing, MacOS ships with bash version 3.x. A newer version is required to run some of our bash scripts, so we install bash 5.x with Homebrew:
brew install bash
Close are restart terminal and check bash version 5.x is working. (Note: Homebrew installs bash 5.x to /usr/local/bin/bash. bash 3.x is still installed at /bin/bash)
bash --version
- Launch Postgres from Applications folder.
- Click the show panel button in the bottom left corner.
- Click the + button to add a new PostgreSQL instance.
- Name the new instance and select version 13 from the dropdown. Leave port as 5432.
- Press 'Create Server' button.
- Optionally, under 'Server Settings' press 'Change password' and set a password. If you do set a password, be sure to add it to your .pgpass file, covered later in this document.
- Press 'Initialize' to start the server.
You should now have a PostgreSQL server running with these default settings:
- Host: localhost
- Port: 5432
- User: your system username
- Database: same as user
- Password: none
Add the following line to ~/.zshrc:
export PATH=$PATH:/Applications/Postgres.app/Contents/versions/13/bin
Then close and restart terminal. You should now be able to run psql from anywhere.
psql --version
To prevent inadvertantly adding and commiting files, the commands git add . and git stage . should be avoided. This can be enforced by adding a wrapper on the git command to your ~/.zshrc file:
git() {
if [ "$1" = "add" -o "$1" = "stage" ]; then
if [ "$2" = "." ]; then
printf "'git %s .' is currently disabled by your Git wrapper.\n" "$1";
else
command git "$@";
fi
else
command git "$@";
fi;
}
Test that the wrapper is working by opening a new terminal and running those two commands from any folder.
Similar to above, install the git-secrets as a tool to avoid accidentally checking secrets into git.
Install using homebrew:
brew install git-secrets
From the advanced configuration, configure the secrets checks for AWS credentials in existing repos and those cloned in the future:
git secrets --register-aws --global
git secrets --install ~/.git-templates/git-secrets
git config --global init.templateDir ~/.git-templates/git-secrets
Create a workspace (e.g. ~/workspace/seattleflu) and clone the three primary repos:
mkdir ~/workspace
mkdir ~/workspace/seattleflu
cd ~/workspace/seattleflu
git clone https://github.com/seattleflu/id3c
git clone https://github.com/seattleflu/id3c-customizations
git clone https://github.com/seattleflu/backoffice
Make sure you can run pipenv sync in the id3c and id3c-customizations folders:
cd ~/workspace/seattleflu/id3c
pipenv sync
pipenv run pytest -v
pipenv run id3c --help
cd ~/workspace/seattleflu/id3c-customizations
pipenv sync
pipenv run pytest -v
We use envdir for managing environment variables. You can set up an env.d directory locally. It will contain individual files for every environment variable, and subdirectories to further organize. You can see one example for the organizational structure in backoffice/id3c-production/env.d.
Create an env.d directory in the same folder:
mkdir ~/workspace/seattleflu/env.d
For this example we'll create a redcap subdirectory containing two environment variables:
mkdir ~/workspace/seattleflu/env.d/redcap
Use a text editor to create a new file ~/workspace/seattleflu/env.d/redcap/REDCAP_API_URL with contents:
https://redcap.iths.org/api/
We store Redcap API tokens using this file naming convention: REDCAP_API_TOKEN_redcap.iths.org_{PROJECT_ID}.
Log in to the REDCap instance, open a specific project, note the project ID (pid) value in the URL, and click "API" from in the sidebar menu. Generate an API token and save the value in a new file ~/workspace/seattleflu/env.d/redcap/REDCAP_API_TOKEN_redcap.iths.org_{PROJECT_ID}
Note: These environment variable files and others can be added later as you need them.
This is an expanded version of the documentation found here
Add PGHOST and PGUSER to ~/.zshrc:
export PGHOST=localhost
export PGUSER=<your system username>
Then close and restart terminal.
Please note that this process can take several hours and is best to run with a fast connection and with battery saving options turned off in System Preferences > Battery > Power Adapter (check "Prevent computer from sleeping automatically when the display is off")
We create a local directory to save the pg_dump files, and specify bash on the refresh-database command to ensure it uses bash 5.x:
mkdir ~/workspace/refresh-db-workdir
cd ~/workspace/seattleflu/backoffice
bash ./dev/refresh-database -d ~/workspace/refresh-db-workdir -x
Note: If you use the same working directory to update the database you should empty it before refreshing again. If you don't clear the directory, this command will utilize the database dump that already exists rather than new production data.
Follow these instructions to create and test Postgres service and password files.
Sqitch is a database change management application.
brew tap sqitchers/sqitch
brew install sqitch --with-postgres-support
ID3C uses Smartystreets for geocoding addresses. Credentials must be provided, and can be added to a new env.d folder:
mkdir ~/workspace/seattleflu/env.d/smartystreets
Use a text editor to create new files ~/workspace/seattleflu/env.d/smartystreets/SMARTYSTREETS_AUTH_ID and SMARTYSTREETS_AUTH_TOKEN. Those values can be found in tne LastPass shared folder.
Each address geocoded incurs a cost so the production server uses cache files to minimize the number of geocoding service requests. To avoid charges when running id3c etl redcap-det commands locally, these cache files should be copied from the production server to your local machine:
mkdir ~/workspace/seattleflu/cache
scp -i [ssh_key_file].pem [email protected]:/home/ubuntu/sfs-cache.pickle ~/workspace/seattleflu/cache/sfs-cache.pickle
scp -i [ssh_key_file].pem [email protected]:/home/ubuntu/scan-cache.pickle ~/workspace/seattleflu/cache/scan-cache.pickle
scp -i [ssh_key_file].pem [email protected]:/home/ubuntu/uw-reopening-cache.pickle ~/workspace/seattleflu/cache/uw-reopening-cache.pickle
To determine which cache file to use with which id3c etl redcap-det project argument, refer to the backoffice crontab file.
These keys will be used to access private Github repos and ssh to the backoffice server.
Follow these instructions to generate your keys and update your Github account with your public key. Your public key will also need to be added to the backoffice server so that you can use connect via ssh.