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Blast_Cache

This is a system for storing, serving and tracking BLAST and PSI_BLAST PSSM files.

Installation

  1. dnf install postgresql-contrib (for hstore extension)
  2. pip install -r requirements/base.txt
  3. Add blast_cache db to postgres CREATE DATABASE blast_cache_db;
  4. Enable hstore extension \c blast_cache_db CREATE EXTENSION hstore;
  5. Create test template for the test db CREATE DATABASE hstemplate; \c hstemplate CREATE EXTENSION hstore; update pg_database set datistemplate=true where datname='hstemplate';
  6. Add blast_cache_user to postgres CREATE USER blast_cache_user WITH PASSWORD ''; ALTER USER blast_cache_user CREATEDB;
  7. Run migrations
  8. Add 'manage.py createsuperuser'

API

  1. GET Requests
  • blast_cache/list/ : List every single entry in the db
  • blast_cache/list/[MD5] : list all unexpired entries in the db with this MD5
  • blast_cache/entry/[MD5]?[param...]=[value]... : retrieve unexpired single unique record given MD5 and uniquely specifying params
  • blast_cache/entry/[MD5]?[param...]=[value]&block=true... : retrieve unexpired single unique record given MD5 and uniquely specifying params and if not present create a record and set it to blocked
  1. POST Requests
  • blast_cache/entry : required fields include

When posting PSSM string data it needs to be escaped properly so that it does not get read as json on submission (see line 98 of run_blast.py), .replace('"', '\"').replace('\n', '\n'). This also means that these escape sequences must be removed when data is retrieved

Required POST parameters

  • name: A short easy to remember identifier for the cache entry
  • md5: The md5 hash of the protein sequence for the cache entry
  • file_type: An integer reflecting the file type; 1: PSSM, 2: CHK
  • blast_hit_count: An integer listing the number of blast hits
  • runtime: An integer listing the blast runtime in seconds
  • data: A dict containing the file_data (required)

Test with

python manage.py test --settings=blast_cache.settings.dev

Start with

python manage.py runserver --settings=blast_cache.settings.dev