Code¶
Note
We are in the process of packaging the system in a docker container to achieve a more reproducible, environment-independent local deployment solution. In the meantime please see our guidelines below which summarie necessary components and steps to run bio.tools.
Source code¶
The source code of the registry is under standard GPL 3.0 license and is available from https://github.com/bio-tools/biotoolsRegistry/.
Architecture¶
The architecture of the registry is designed around the principle of decoupling frontend from the backend in order to eliminate performance bottlenecks at scale. The backend serves the data through the RESTful APIs which are in turn consumed by the the frontend SPA (Single-Page Application). The main advantage of this paradigm is that the frontend uses the exact same API calls that any user can invoke in order to create their own customized interface. The overall goal of scalability can be achieved by hosting the components independently (master database, replicated cache layer and static frontend code in a CDN - Content Delivery Network - such as Cloudflare or Akamai).
Components¶
You only need Docker to run bio.tools locally.
Installing bio.tools on your system¶
The local (development) installation is done via Docker. Other than Git (and a text editor), nothing else is required to run and write code for bio.tools.
1. Download and Install Docker¶
Docker main installation page¶
https://docs.docker.com/install/
Note
You will need to create a Docker Hub account.
Windows
https://docs.docker.com/docker-for-windows/install/
Note
Read the “What to know before you install” information to see if Docker Destktop for Windows can be installed on your system. If your system does not meet the requirements to run Docker Desktop for Windows, you can install the legacy Docker Toolbox.
MacOS
https://docs.docker.com/docker-for-mac/install/
CentOS
https://docs.docker.com/install/linux/docker-ce/centos/
Debian
https://docs.docker.com/install/linux/docker-ce/debian/
Fedora
https://docs.docker.com/install/linux/docker-ce/fedora/
Ubuntu
2. Clone the repo¶
Using HTTPS¶
git clone https://github.com/bio-tools/biotoolsRegistry.git
Using SSH¶
git clone git@github.com:bio-tools/biotoolsRegistry.git
Go into the folder in which you cloned the bio.tools repo. By default it will be called biotoolsRegistry
: (e.g. cd biotoolsRegistry
or cd /home/user/coding/biotoolsRegistry
)
3.0 Inside the bio.tools repo¶
Note
The Docker setup will require up to 5 GB of disk space. The bio.tools data will also add to this.
3.0.1 Build the necessary Docker images¶
docker-compose build
The above command will download / build all the Docker images required for bio.tools to run on your local machine.
The images built can be seen by running: docker image ls
and are:
biotools/frontend
(~ 827MB)
biotools/backend
(~ 1.12GB)
mysql
(~ 205MB)
(will show up after running 3.0.2)elasticsearch
(~ 486MB)
(will show up after running 3.0.2)python
(~ 925MB)
node
(~ 650MB)
3.0.2 Create and run the Docker containers¶
docker-compose up
The above command will create and run the required containers:
biotools-mysql
biotools-elasticsearch
biotools-backend
(depends onbiotools-mysql
andbiotools-elasticsearch
)biotools-frontend
(depends onbiotools-backend
)
Note
After running the docker-compose up
command, the containers will start and will output log messages which you can see in your terminal window. In order for the containers to keep running this window needs to stay open. You will need to open new terminal windows/tabs for other operations.
docker-compose up
will also build the images if they do not exist, but in order to be sure your latest source code and image changes are running make sure you run docker-compose build
beforehand
Too see the running containers run: docker container ls
3.1 The short(er) setup¶
Run the steps below in the root folder of the Git project (e.g. biotoolsRegistry
)
3.1.1 Make migrations¶
docker exec biotools-backend python manage.py makemigrations
Make Django migrations from the exiting models. Executed on the biotools-backend
container. If you get the No changes detected
message it means that you are up to date.
3.1.2 Migrate to the DB¶
docker exec biotools-backend python manage.py migrate
Create necessary tables and other DB objects from the migrations. Executed on the biotools-backend
container. If you get the No migrations to apply.
message it means that you are up to date.
3.1.3 Copy initial (seed) DB¶
docker cp initial_db.sql biotools-mysql:/root
Copies the initial_db.sql
SQL file into the biotools-mysql
container (where the MySQL database server runs) into the /root
folder.
3.1.4 Copy initial DB load script file¶
docker cp load_initial_db.sh biotools-mysql:/root
Copies the load_initial_db.sh
into the biotools-mysql
container. This file will run the MySQL commands used to load the database described in initial_db.sql
3.1.5 Execute initial DB load script file¶
docker exec biotools-mysql bash /root/load_initial_db.sh
Executes the load_initial_db.sh
file in the biotools-mysql
container which loads the initial (seed) DB data.
Note
The initial DB contains 11 tool annotations, a superuser (username: biotools
, password: biotools
), an initial test
subdomain and the necessary EDAM files. See 3.1.8 for more.
3.1.6 Purge Elasticsearch¶
docker exec biotools-backend python manage.py es_purge
Purges (clears) any data in the Elasticsearch index. Executed in the biotools-backend
container which communicates with the biotools-elasticsearch
container.
3.1.7 Regenerate Elasticsearch¶
docker exec biotools-backend python manage.py es_regenerate
Takes all the tools, subdomains annotations etc. in the DB and creates the equivalent entries in the Elasticsearch index. Executed in the biotools-backend
container.
3.1.8 Done¶
At this point you can go to http://localhost:8000 to see the local bio.tools homepage.
The test
subdomain can be viewed at http://test.localhost:8000
You can login with the existing superuser (user: biotools
, password: biotools
).
All running Docker containers can be stopped by running: docker-compose down
from the root Git folder. This will preserve the data in the MySQL database and Elasticsearch. To reinstantiate everything again run: docker-compose up
.
Only need to run docker-compose build
once at the beginning or if changes are made to the bio.tools Docker settings files.
If you wish to remove the data along with the containers run: docker-compose down -v
which will also remove the Docker volumes which preserve the MySQL and Elasticsearch data.
3.2 The longer setup¶
This is an alternative to 3.1 in which some of the steps were contained in the initial DB files. This will start with no data.
Run the steps below in the root folder of the Git project (e.g. biotoolsRegistry
)
3.2.1 Make migrations¶
docker exec biotools-backend python manage.py makemigrations
Make Django migrations from the exiting models. Executed on the biotools-backend
container.
3.2.2 Migrate to the DB¶
docker exec biotools-backend python manage.py migrate
Create necessary tables and other DB objects from the migrations. Executed on the biotools-backend
container.
3.2.3 Create a superuser¶
docker exec -it biotools-backend python manage.py createsuperuser
Prompts the creation of a superuser, need to input superuser name, email (optional) and password. Executed on the biotools-backend
container.
3.2.4 Setup EDAM ontology¶
docker exec biotools-backend bash /elixir/application/backend/data/edam/update_edam.sh
Download EDAM ontology and push it to the DB. Can also be used to update to new EDAM version. The file which indicates the EDAM version is <git_project_root>/backend/data/edam/current_version.txt
, e.g. biotoolsRegistry/backend/data/edam/current_version.txt
3.2.5 Copy helper tables SQL¶
docker cp update_site_settings.sql biotools-mysql:/root
Copies the update_site_settings.sql
SQL file into the biotools-mysql
container (where the MySQL database server runs) into the /root
folder. This file contains SQL instructions used to create helper tables and settings for the project.
3.2.6 Copy script file to run helper tables¶
docker cp update_site_settings.sh biotools-mysql:/root
Copies the update_site_settings.sh
into the biotools-mysql
container. This file will run the MySQL commands described in update_site_settings.sql
3.2.7 Execute script file¶
docker exec biotools-mysql bash /root/update_site_settings.sh
Executes the update_site_settings.sh
file in the biotools-mysql
container which loads the helper tables and settings in the DB.
3.2.8 Purge Elasticsearch¶
docker exec biotools-backend python manage.py es_purge
Purges (clears) any data in the Elasticsearch index. Executed in the biotools-backend
container which communicates with the biotools-elasticsearch
container.
3.2.9 Regenerate Elasticsearch¶
docker exec biotools-backend python manage.py es_regenerate
Takes all the tools, subdomains annotations etc. in the DB and creates the equivalent entries in the Elasticsearch index. Executed in the biotools-backend
container.
3.1.10 Done¶
At this point you can go to http://localhost:8000 to see the local bio.tools homepage.
Login with the user created in 3.2.3
No tools or subdomains are available, add tools at http://localhost:8000/register and subdomains at http://localhost:8000/subdomain
All running Docker containers can be stopped by running: docker-compose down
from the root Git folder. This will preserve the data in the MySQL database and Elasticsearch. To reinstantiate everything again run: docker-compose up
.
Only need to run docker-compose build
once at the beginning or if changes are made to the bio.tools Docker settings files.
If you wish to remove the data along with the containers run: docker-compose down -v
which will also remove the Docker volumes which preserve the MySQL and Elasticsearch data.
4. Useful information¶
4.0 Basic usage¶
After completing steps 1-3 above, the only required commands for basic use are
docker-compose up
and
docker-compose down
and perhaps
docker-compose down -v
4.1 Local dev¶
After running docker-compose up
you will see a number of log messages. These messages come from the running containers:
- biotools-mysql (MySQL logs)
- biotools-elasticsearch (Elasticsearch logs)
- biotools-backend (Mostly Apache logs, sometimes Python logs)
- biotools-frontend (Gulp logs)
4.1.1 Backend dev¶
The biotools-backend
container is based on an image which uses an Apache server. The logs from biotools-backend
come from Apache or sometimes from Python.
Note
Changes in Python/Django/backend files will be reflected in the biotools-backend
container, BUT because of how Apache works, the changes won’t be reflected in your browser http://localhost:8000
until Apache is reloaded. In order to see the changes in the reflected in the browser you need to run:
docker exec biotools-backend /etc/init.d/apache2 reload
Remember to run the above command whenever you want to see your code changes reflected in your local bio.tools.
Bringing the containers down and up agail will also work, but this takes significantly longer. The above command is almost instant.
Most issues with the backend code will be reflected in the browser at http://localhost:8000/api/{some_path}
, e.g. http://localhost:8000/api/tool or http://localhost:8000/api/jaspar etc.
See https://biotools.readthedocs.io/en/latest/api_reference.html or Django route files (urls.py
) for more API endpoints.
4.1.2 Frontend dev¶
The biotools-frontend
container outputs logs from gulp
( https://gulpjs.com/ ) which bundles all frontend JavaScript and CSS code.
Every time you change and save a .js
or .css
file in the frontend, gulp will re-bundle everything automatically. This implies that all changes in the frontend are reflected automatically in thr browser, unlike for the backend.
Note
If you have a syntax error in your JavaScript or CSS files, gulp will fail and you won’t see any changes reflected in the browser. So, if your changes are not reflected, look at the biotools-frontend
logs of gulp which will indicate if you made a syntax error in your code.
4.2 Update EDAM¶
Similarly to section 3.2.4, in order to update to the latest EDAM version (or just use a different EDAM version) the update_edam.sh
needs to be executed on the biotools-backend
container.
The version number used for updating EDAM is specified in the file:
<git_project_root>/backend/data/edam/current_version.txt
In order to update to the latest EDAM version (e.g. 1.23
) edit the current_version.txt
file to store the value 1.23
, save the file and run:
docker exec biotools-backend bash /elixir/application/backend/data/edam/update_edam.sh
The script file will download the specific EDAM version .owl file from https://github.com/edamontology/edamontology and execute the:
python /elixi/application/manage.py parse_edam
command in the biotools-backend
container.
Note
The current_version.txt
file is tracked by Git and any changes involving EDAM versions other than latest should not be pushed to the main branches of the repo.
4.3 Local email setup¶
Important to note that the email system used to send emails regarding account creation and password reset will not work as intended out of the box .
In order for the emails to work you need to provide credetials (email, password, smtp settings) in the backend/elixirapp/settings.py
file. bio.tools production uses Zoho mail (http://zoho.com) which currently works well with our setup.
The easy way would be to make a Zoho email account and use that email information to make the email functionality run. Gmail and Yahoo were tried and the connections are blocked by Gmail and Yahoo because of security reasons. This is because Gmail and Yahoo don’t accept a simple username-password login and require more strict settings. Feel free to implement this in your bio.tools instance.
4.4 Docker notes¶
Build bio.tools Docker images¶
docker-compose build
Run bio.tools containers¶
docker-compose up
Stop bio.tools containers¶
docker-compose down
Stop bio.tools containers and remove data¶
docker-compose down -v
View running containers¶
docker container ls
View all containers¶
docker container ls -a
Remove stopped containers¶
docker container rm <CONTAINER_ID>
or
docker container rm <CONTAINER_ID1> <CONTAINER_ID2> <CONTAINER_ID3>
Force remove containers¶
docker container rm -f <CONTAINER_ID>
or
docker container rm -f <CONTAINER_ID1> <CONTAINER_ID2> <CONTAINER_ID3>
Prune containers (Remove all stopped containers)¶
docker container prune
View images¶
docker image ls
Remove image¶
docker image rm <IMAGE_ID>
or
docker image rm <IMAGE_ID1> <IMAGE_ID2> <IMAGE_ID2>
(will not work if containers are running this image)
Enter a container and run commands¶
Any of the bio.tools runnning containers can provide a bash terminal to run commands inside the containers (similar to docker exec
). Examples of the commands are:
- docker exec -it biotools-mysql bash
- docker exec -it biotools-elasticsearch bash
- docker exec -it biotools-backend bash
- docker exec -it biotools-frontend bash
As an example, to view the info in a MySQL database table run:
docker exec -it biotools-mysql bash
- In container:
mysql -u elixir -p
(password is by default123
) - In MySQL:
use elixir;
SELECT * FROM elixir_resource WHERE visibility = 1;
bio.tools Docker settings files:¶
Backend build config file
<git_project_root>/backend/Dockerfile
Backend dockerignore file
<git_project_root>/backend/.dockerignore
Frontend build config file
<git_project_root>/frontend/Dockerfile
docker-compose YAML config file
<git_project_root>/docker-compose.yml
Docker documentation:¶
API Guidelines¶
You can also check out our API instructions at the links below: