Installing CALLISTO

Pre-requisites

• Callisto can be installed on your laptop (gnu/linux based) for tests and development
• Callisto should be installed on a gnu/linux based server (tested on Ubuntu) for production
• Callisto lives in different lxd containers, SO you should first install lxd
• Callisto uses ansible to deploy the programs in the lxc containers: ansible should be installed on the host
• The Callisto software should be downloaded on the host

Installing lxd:

First install snap on your system (using apt-get, yum etc)

Then install lxd:

sudo snap install lxd

Configure lxd:

lxd init

Here is a mini-tutorial about lxc:

To enter the CallistoPortal container:

lxc exec CallistoPortal bash

To exit from the CallistoPortal container:

exit

or

CTRL-D

A more complete documentation about lxd can be found here: https://ubuntu.com/tutorials/introduction-to-lxd-projects#1-overview

Configure lxd to be able to share directories:

You should prepare the mapping between the uid/gid in the host and in the containers (you'll have to restart lxd daemon, thus all containers will be restarted)

# printf "lxd:$(id -u):1\nroot:$(id -u):1\n" | sudo tee -a /etc/subuid
lxd:1000:1
root:1000:1

# printf "lxd:$(id -g):1\nroot:$(id -g):1\n" | sudo tee -a /etc/subgid
lxd:1000:1
root:1000:1

sudo systemctl restart snap.lxd.daemon

Installing Ansible:

Callisto uses ansible to deploy the application on several lxd containers (centOs7 based). So Ansible should be installed on the host (release 2.9.11 required):

sudo -H pip3 install ansible==2.9.11

Downloading Callisto:

git clone https://github.com/calmip/callisto

in the following, $WORKDIR means: the directory where you cloned callisto

Installing Callisto (base containers)

Copy the file vars.yml.dist:

cd $WORKDIR/install
cp vars.yml.dist vars.yml

Edit the file vars.yml:

• choose laptop or server for the variable callisto_living_on
• Choose and write credentials for the use of Allegro software (allegro_user and allegro_password)
• ssh_wanted: if true, your ssh public key shall be copied to the containers, to easily enter the containers. This is only convenient if you are a developer. Default is false
• If installing on server, there are other variables to set (callisto_url, mail addresses and some other stuff)

Managing the certificates:

• If installing on your laptop, you can use the self-signed certificates:

  cd $WORKDIR/install
  cp roles/proxy/files/cert.pem.dist roles/proxy/files/ssl/cert.pem
  cp roles/proxy/files/key.pem.dist  roles/proxy/files/ssl/key.pem
  

• If installing on a server, you should get a secure certificate for the domains (a *.{{ callisto_url }} certificate is OK):

  • {{ callisto_url }}
  • dataverse.{{ callisto_url }}
  • allegro.{{ callisto_url }}
  • Copy the certificate, the key and the chain to the directory roles/proxy/files/ssl
  • See also the file certificates/README.txt (there is a certificate to get for Shibboleth configuration)

Run the following command to create the containers and install inside the depencies :

cd $WORKDIR/install
ansible-playbook -i inventory callisto.yml -K

Partial installs can be done with the --tags switch (have a look to callisto.yml to know the tags):

cd $WORKDIR/install
ansible-playbook -i inventory --tags proxy callisto.yml -K

share the callisto directory with CallistoPortal:

The directory $WORDIR/callisto must be shared by the container CallistoPortal under /usr/local/callisto. this is done by the following command:

cd $WORKDIR/install
bash shareDir.bash

Now, if you modifiy anything from the host under directory $WORKDIR/callisto, your modifications will be visible from the CallistoPortal container, under the directory /usr/local/callisto

Installing Callisto (the code):

Create and edit the callisto configuration file. Please choose a user name and a password as Allegro administrator.

cd $WORKDIR/callisto/etc
cp callisto_conf.cfg.dist callisto_conf.cfg
vi callisto_conf.cfg 

Installing dataverse:

Dataverse should be installed inside the container CallistoDataverse:

lxc exec CallistoDataverse bash

You live now in a CentOs 7 computer, please install dataverse as explained here: https://dataverse.harvard.edu/

Using the Dataverse ansible role:

You may try to use the ansible role provided by Dataverse; you shoud stay on the host an proceed as follows:

cd $WORKDIR/..
git clone https://github.com/GlobalDataverseCommunityConsortium/dataverse-ansible.git dataverse
cd dataverse
git checkout 3b0277a0ad5bcb717dd2fd186fe9162fd157bfe9

Change the file called inventory as follows:

[dataverse]
CallistoDataverse ansible_connection=lxd

Return to base directory and run the command:

cd $WORKDIR/../dataverse
ansible-playbook -v -i dataverse/inventory dataverse/dataverse.pb -e dataverse/defaults/main.yml -K

Installing the demonstration repository in dataverse:

Enter the Dataverse container:

lxc exec CallistoDataverse bash

Execute the following commands inside the container:

cd /
tar xvfz 10.5072.tgz
systemctl stop payara 
dropdb -U postgres dvndb 
createdb -U postgres dvndb 
psql -U postgres dvndb -f 10.5072.sql
systemctl start payara 
curl http://localhost:8080/api/admin/index/clear 
curl http://localhost:8080/api/admin/index

Installing Allegro:

Enter the Allegro container:

lxc exec CallistoAllegro bash 

Get the Allegro rpm:

wget https://franz.com/ftp/pri/acl/ag/ag7.0.3/linuxamd64.64/agraph-7.0.3-1.x86_64.rpm

Install the rpm:

rpm -i agraph-7.0.3-1.x86_64.rpm

Configure Allegro:

/usr/bin/configure-agraph
(Doing so, make sure to use the password and user for agraph that you specified in callisto vars.yml configuration file)    

Enable Allegro for automatic start:

chkconfig agraph on

Start Allegro:

systemctl start agraph

Configuring your dataverse API Key for ontological datasets update

In the CallistoPortal container, go to /usr/local/callisto/bin In DataSetsToAllegro.py, update line 52 replace API_TOKEN = "" by API_TOKEN = "YOUR DATAVERSE ADMIN API TOKEN"

Creating your first workflow

Read the document (in french) inside the directory callisto/doc

Running Callisto

• Point your browser to the callisto url defined in vars.yml (variable callisto_url)

Running on your laptop:

When visiting https://callisto-local.mylaptop the FIRST TIME your browser will send a warning because there is an autosigned certificate: Please accept the risk

Then click the menu link "valid dataverse certif" to validate the autosigned certificate of the dataverse url. This is required to be able to use dataverse from an iframe, as it is the normal use of dataverse in Callisto

Your browser will not warn you anymore

License

Callisto is covered by the GNU AFFERO GENERAL PUBLIC LICENSE version 3 Please read the LICENSE.txt file

Author Information

Thierry Louge [email protected] Emmanuel Courcelle [email protected]