Django server for Fragalysis with DRF API and loaders for data. Has components to serve React web-app.
The stack consists of three services, running as containers: -
- a Postgres database (note: this used to be MySQL)
- a neo4j graph database
- the fraglaysis stack
The stack is formed from code resident in a number of repositories. Begin by forking repositories you anticipate editing (although you really want to consider forking all the repositories as this is a relatively low-cost operation).
The repositories are:
- Docker
- Docker-compose
- Git
1.Create project directory, e.g.
mkdir fragalysis
2.Clone repositories inside your project's directory
You can clone original xchem repositories or your forked e.g. m2ms and checkout any branch if necessary
git clone https://github.com/xchem/fragalysis-backend.git
git clone https://github.com/xchem/fragalysis-frontend.git
git clone https://github.com/InformaticsMatters/dls-fragalysis-stack-openshift.git
Note: To successful build, it should exist following directories from repository cloning. Frontend is also important, because DJANGO server will serve this directory!
fragalysis/fragalysis-frontend/
fragalysis/fragalysis-backend/
fragalysis/dls-fragalysis-stack-openshift/
3.Create some key data directories
In fragalysis/ directory run script to create data directory structure
mkdir -p data/input/django_data/EXAMPLE
mkdir -p data/neo4j/data
mkdir -p data/neo4j/logs
mkdir -p data/stack/media
mkdir -p data/stack/logs
mkdir -p data/media/compound_sets
mkdir -p data/postgre/data
4.Populating database
Copy to fragalysis/data/input/django_data/EXAMPLE your PDB data, before you can launch the application.
If not exists file fragalysis/data/input/django_data/EXAMPLE/TARGET_LIST create it and content with list of your data, for example:
Mpro, NUDT7A,...
The best approach is to spin-up the development stack (locally) using
docker-compose and then shell into the Django (stack). For example,
to make new migrations called "add_job_request_start_and_finish_times"
for the viewer's models run the following: -
docker-compose up -d
docker-compose exec stack bash
Then from within the stack...
python manage.py makemigrations viewer --name "add_job_request_start_and_finish_times"
Exit the container and tear-down the deployemnt: -
docker-compose down
The project uses pre-commit to enforce linting of files prior to committing them to the upstream repository.
To get started review the pre-commit utility and then set-up your local clone by following the Installation and Quick Start sections of the pre-commit documentation.
Ideally from a Python environment...
pip install --upgrade pip
pip install -r build-requirements.txt
pre-commit install -t commit-msg -t pre-commit
Now the project's rules will run on every commit.
Start Fragalysis stack (All infrastructure - databases + populating data)
docker-compose -f docker-compose.dev.yml up -d
Please wait, it takes a minute until all containers are fully started.
Test if we are running at http://localhost:8080
If needed stop containers
docker-compose -f docker-compose.dev.yml down
Note: The first run will be probably not successful. To fix after first run:
- Delete the 'mysql_data' folder located in the data folder (Step 3)
- Delete the migrations by running the commands below in the project directory (Step 1)
find . -path "*/migrations/*.py" -not -name "__init__.py" -delete
find . -path "*/migrations/*.pyc" -delete
- In the 'fragalysis-frontend' folder rerun the docker compose command another two times
docker-compose -f docker-compose.dev.yml up
The first you need to have upload key.
connect to web_dock service and run following script
python manage.py shell
from viewer.models import CSetKeys
new_key = CSetKeys()
new_key.name = 'test'
new_key.save()
print(new_key.uuid)
It is important to have key in following format (with -)
f8c4ea0f-6b81-46d0-b85a-3601135756bc
Visit localhost:8080/viewer/upload_cset - for computed sets
Visit localhost:8080/viewer/upload_tset - for targets
The target name is for example Mpro, select sdf file and you don't need a pdb file.
Before upload generate upload key.
In settings.py, the value of DEBUG is set to False by default. This can be set locally by adding the
following line to the web_dock section of your docker_compose file:
DEBUG_FRAGALYSIS: True
or adding the following line to the AWX template:
stack_debug_fragalysis: True
Note that this will also enable logging on the stack, so when coding you can use the logger and then jump on the webdock and check the logfile on /logs/ (although this doesn't work from celery yet).
In settings.py, this is controlled by setting the value of SENTRY_DNS. To enable it, you need to set it to a valid
Sentry DNS entry. For Diamond, this can be set locally by adding the
following line to the web_dock section of your docker_compose file:
SENTRY_DNS: https://27fa0675f555431aa02ca552e93d8cfb@o194333.ingest.sentry.io/1298290
or adding the following line to the AWX template:
stack_backend_sentry_dsn: https://27fa0675f555431aa02ca552e93d8cfb@o194333.ingest.sentry.io/1298290
As the application evolves several design documents have been written detailing improvements. These may be useful for background reading on why decisions have been made.
The documents will be stored in the /design_docs folder in the repo. Current docs are listed below: