Production application

• Instal --

    - git clone  https://github.com/vinay-ebi/production_app.git
    - cd production_app
    - python setup.py  install
    - pip install -r requirements.txt
    - pip install .

• Run application

    - production_app

• Example:

    To use swager UI: http://localhost:8090/ensembl/handover

• Run Test Case

    - python -m pytest

• Build docker image

---

• sudo docker build -t productionsrv:latest -f docker/Dockerfile .

• Run Docker Container

  • sudo docker run --network=host -it productionsrv:latest -r handover -p 5000

-Submit and run background jobs with Rabbitmq, celery

• Install

---

- sudo apt-get install rabbitmq-server
- sudo service rabbitmq-server start
- pip install celery

• Start rabbitmq message broker, celery worker and flask

---

- cd production_app	
- celery -A app.celery worker -Q handover --loglevel=info -n 'worker1%h'
- celery -A app.celery worker -Q datacheck --loglevel=info -n 'worker2%h'
- celery -A app.celery worker -Q dbcopy --loglevel=info -n 'worker3%h'
- celery -A app.celery worker -Q metadata  --loglevel=info -n 'worker4%h'
- production_app_api -p 8090 

-monitor celery worker using flower

• pip install flower -celery -A production_app.app_celery.celery flower -http://localhost:5555

• Example:

  To use swager UI: http://localhost:8090/app/

  • 1: submit job to queue

        
  http://localhost:5000/app/jobs
    
    	Return the status and task_id submitted to queue
    	---------------------------------
    	-{ "status": "PENDING",  "task_id": "99081de1-2290-420d-96aa-0ca4c7221b22"}
  

  • 2: Get status and result for submitted job

Hive initiation

• RUN HIVE config file to create HiveDB :

init_pipeline.pl Bio::EnsEMBL::Production::Pipeline::PipeConfig::CopyDatabase_conf -pipeline_url 'mysql://vinay:vinay@localhost/vinay_copy_database2' -hive_force_init 1

-RUN bekeeper.pl to submit the jobs

beekeeper.pl -url "mysql://vinay:vinay@localhost/vinay_copy_database2" -sync --keep_alive -sleep 0.5

-export Hive database URL used by production_app service

export SERVER_URIS_FILE=/home/vinay/Documents/Ensembl-Master/Projects/P3_rabbitmq_example/test_the_ensembl_srv/ensembl-prodinf-srv/server_uris.json
export HIVE_URI=mysql://vinay:vinay@localhost/vinay_copy_database2