README.md

OrderlyWeb / orderly setup for ncov-ic

Set up a server

Currently using Ubuntu 18.04. During the installation there is an option along the lines of "allocate 4G to this drive" which it is important to change to "allocate max to this drive".

Install docker

Install docker following approach in montagu-machine

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository \
         "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"
sudo apt-get update && sudo apt-get install -y docker-ce
sudo usermod -aG docker rich

Add a server user

Create a server user - best done with adduser (rather than useradd)

sudo apt-get install -y pwgen
SERVER_PASSWORD=$(pwgen 30 1)
vault write /secret/ncov/server/password value=$SERVER_PASSWORD
sudo adduser --quiet --disabled-password server
echo "server:$SERVER_PASSWORD" | sudo chpasswd
sudo usermod -aG docker server
sudo usermod -aG sudo server

Configure vault on the server

Install vault on the target machine following instructions in montagu-machine

vault_version=vault_1.0.3
sudo apt-get install -y unzip
wget https://releases.hashicorp.com/vault/${vault_version}/$vault_zip
unzip $vault_zip
chmod 755 vault
sudo cp vault /usr/bin/vault
rm -f $vault_zip vault

And configure a policy for our group:

vault policy write ncov_read ncov-vault.hcl
vault write auth/github/map/teams/ncov value=ncov_read

Add the ssl certificates into the vault

unzip ncov_cert.zip
cat ncov_dide_ic_ac_uk.crt \
  RootCertificates/QuoVadisOVIntermediateCertificate.crt \
  RootCertificates/QuoVadisOVRootCertificate.crt \
  > ncov.crt
vault write secret/ncov/proxy/ssl_certificate [email protected]
vault write secret/ncov/proxy/ssl_private_key [email protected]

Create a GitHub organisation

This project used ncov-ic for the organisation. Someone needs to get hold of github to request an academic upgrade to enable private repositories current documentation on this.

Prepare an orderly repo

Based off, for now, the most recent ebola-outputs repo. Deleted the .git directory, plus all content from src, searched for terms that referred to the ebola outbreak and replaced them with appropriate ones for 2019-nCoV. Resulting skeleton repo is here.

Add a deploy key to this repository (and to the vault) by running

./scripts/add_deploy_key

and following the instructions

Create an oauth app

Two apps are needed - one for "real" and one for testing.

Instructions are on the orderly-web repo

• GitHub Settings -> Developer Settings -> New OAuth App (or go to https://github.com/organizations/ncov-ic/settings/applications/new)
• Application name should be the human readable name of the group (e.g., 2019-nCoV, MRC-GIDA, Imperial College)
• Both the homepage URL and the Authorization callback URL should be the name of the orderly instance (https://ncov.dide.ic.ac.uk or https://ncov.dide.ic.ac.uk:1443)
• The next page displays the secrets - set those within the vault

vault write secret/ncov/oauth/real \
  id=<id> \
  secret=<secret>

and

vault write secret/ncov/oauth/testing \
  id=<id> \
  secret=<secret>

Create an orderly container

Starting from the ebola-orderly container, search and replace "ebola" strings and replace as appropriate, and push up as ncov-ic/ncov-orderly

That needs building on TeamCity. The easiest way was to go into the Ebola Orderly project and select "Copy project" from the "Actions" menu, then edit the VCS root.

Create a new Docker Hub account. Hyphens can't be used, so I used ncovic. Add the vimcrobot user to the organisation so that images can be pushed from TeamCity.

Create the orderly web configuration

Starting from the ebola-orderly-web, replace all uses of ebola and update organisations appropriately.

Create the main server

git clone https://github.com/ncov-ic/ncov-orderly
git clone https://github.com/ncov-ic/ncov-orderly-web
sudo apt-get install -y python3-pip
pip3 install --user orderly-web
echo 'export PATH=$PATH:~/.local/bin' >> ~/.profile
cd ncov-orderly-web
orderly-web start config

After a minute or two the commands will complete and you can log in at https://ncov.dide.ic.ac.uk

When authorising the OAuth application, be sure to grant it access to the organisation that you are used for auth (as specified in config/orderly-web.yml)

Create the staging server

Starting from the staging, replace all uses of ebola and update organisations appropriately.

Follow the instructions in the README.md to:

• Install vagrant and virtualbox
• Make sure that the BIOS supports virtualisation
• Bring up the VM

git clone https://github.com/ncov-ic/staging staging
cd staging
sudo ./provision/setup-vagrant
sudo ./provision/setup-vault
./scripts/vault-prepare
vagrant up
cp scripts/ssh-testing ~server

After a minute or two the commands will complete and you can log in at https://ncov.dide.ic.ac.uk:1443

When authorising the OAuth application, be sure to grant it access to the organisation that you are used for auth (as specified in config/orderly-web.yml)

Users

All users need to provide a project administrator (Rich or Nasuko) a GitHub username and one or more ssh public key.

• GitHub user name: Go to go to github.com and make sure you are logged in. Your username will be shown in the top left below the github logo, or click the avatar in the top right and it will say "Signed in as yourname".
• SSH public key: This is something we can use to verify your identity in a couple of situations.
  • Mac and Linux users - if you have a file as "~/.ssh/id_rsa.pub" send that (you can display this file by running cat ~/.ssh/id_rsa.pub) and copying and pasting the result. If you do not have one, run ssh-keygen, accept the default location and add a password when prompted. Then copy the id_rsa.pub file as above.
  • Windows users follow these instructions to generate your keypair

Please send these via the 2019-nCoV Slack if possible as a Direct Message.