frahik/Mutant_DNA_Sequencer

Mutant DNA sequencer

Odoo Python Module to verify if a DNA sequence is from Mutant or Human

Author

• Francisco Javier Luna Vázquez <frahik@gmail.com>

Installation

Requirements

You need to have the following:

• Odoo Community
• Python 3.8 or later
• Numpy == 1.23.1
• coverage

Run on local

./odoo-bin -i mutant_dna_detector --addons-path <directories>

• --addons-path <directories>: comma-separated list of directories in which modules are stored. These directories are scanned for modules. More information at: Odoo Cli

Run the tests

./odoo-bin -i mutant_dna_detector --test-enable --test-tags dna_sequencer --stop-after-init

Check the coverage

coverage run --source=<path_to_module> --omit="*/__init__.py,*/__manifest__.py,*/tests/*,*/controllers/*" <path_to_odoo_directory>/odoo-bin -d odoo --xmlrpc-port=8012 -u mutant_dna_detector --test-enable --log-level=test --stop-after-init

coverage report -m
# Name                                                                             Stmts   Miss  Cover   Missing
# --------------------------------------------------------------------------------------------------------------
# <path>/Mutant_DNA_Sequencer/mutant_dna_detector/models/dna_sequencer.py      60      5    92%   37-38, 45-46, 115
# --------------------------------------------------------------------------------------------------------------
# TOTAL                                                                               60      5    92

API

Mutant

Use the mutant url to check if a DNA sequence is from a Human or Mutant.

POST	/mutant

Sample Request:

curl -i \
    -H "Content-Type: application/json" \
    -X POST -d '{"dna":["ATGCGA","CAGTGC","TTATGT","AGAAGG","CCCCTA","TCACTG"]}' \
    http://localhost:8069/mutant

Body:

• dna list of strings (required): The server stores the DNA sequence to determine if it is from a human or mutant

Sample Response:

{
    "jsonrpc": "2.0",
    "id": null,
    "result": {
        "status": "403 Forbidden: You don't have the permission to access the requested resource. It is either read-protected or not readable by the server."
    }
}

Response:

A successful request returns a JSON response body

• jsonrpc string: The version of the jsonrpc api
• id int: Null key.
• result:
  • status string: The Response of the server, the possible values are:
    • 200 OK: If the DNA provided is from a human
    • 400 Bad Request: The browser (or proxy) sent a request that this server could not understand.: If the DNA provided doesn't correspond to a DNA possible values (A, C, T, G)
    • 403 Forbidden: You don't have the permission to access the requested resource. It is either read-protected or not readable by the server.: If the DNA provided is from a mutant.
    • 422 Unprocessable Entity: The request was well-formed but was unable to be followed due to semantic errors.: If the length of columns differs and no mutant sequence was found in the rows of the DNA provided.

Stats

Use the stats url to check the number of dna queries performed,

GET	/stats

Sample Request:

curl -i \
    -H "Content-Type: application/json" \
    -H "Accept: application/json" \
    -X GET -d {} \
    http://localhost:8069/stats

Body:

• Require a empty json -d {}

Sample Response:

{
    "jsonrpc": "2.0",
    "id": null,
    "result": {
        "count_mutant_dna": 17,
        "count_human_dna": 7,
        "ratio": 2.4285714285714284
    }
}

Response:

A successful request returns a JSON response body

• jsonrpc string: The version of the jsonrpc api
• id int: Null key.
• result:
  • count_mutant_dna int: The amount of processed DNA that corresponds to mutants
  • count_human_dna int: The amount of processed DNA that corresponds to humans
  • ratio float: The ratio indicates how many times DNA mutant it's found by one of a DNA human.

Licenses

This repository is licensed under LGPL-3.0.