server.py

#!env/bin/python
#
# Copyright (c) 2022 Be The Match.
#
# This file is part of BLEAT
# (see https://github.com/nmdp-bioinformatics/b-leader).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
from flask import Flask, jsonify, request
from flask_restplus import Api, Resource, fields
from bleader.hla_b import HlaBAllotype, HlaBGenotype
from bleader.match import HlaBAllotypeMatch, HlaBGenotypeMatch
from bleader.mapper import LeaderMapper
from bleader.map import LeaderMap

app = Flask(__name__)
api = Api(app=app)
ns_type = api.namespace(
    "b-leader-classification",
    description="Classify the leader types of HLA-B allotype(s) and genotype(s).",
)
ns_match = api.namespace(
    "b-leader-match",
    description="Classify the leader match status of a HLA-B genotype against HLA-B genotype(s).",
)

allele_model = api.model(
    "allele", {"allele": fields.String(example="B*07:02:01/B*07:02:02", required=True)}
)


@ns_type.route("/allotype/<string:hla_allotype_input>")
class LeaderAllotype(Resource):
    def get(self, hla_allotype_input):
        """
        returns leader-peptide allotype(s) of HLA-B allele(s)log fie
        """
        try:
            hla_allotypes = [
                allo.strip() for allo in list(set(hla_allotype_input.split(",")))
            ]
            results = []
            mapper = LeaderMapper()
            for hla_allotype in hla_allotypes:
                results.append(mapper.get_leader_allotype_info(hla_allotype))
            return jsonify(results)
        except Exception as e:
            return e.__dict__, 500


@ns_type.route("/allotype")
class LeaderAllotype(Resource):
    @api.expect(allele_model)
    def post(self):
        """
        returns leader-peptide allotype(s) of HLA-B allele(s)log fie
        """
        try:
            hla_allotype_input = request.json["allele"]
            hla_allotypes = [
                allo.strip() for allo in list(set(hla_allotype_input.split(",")))
            ]
            results = []
            mapper = LeaderMapper()
            for hla_allotype in hla_allotypes:
                results.append(mapper.get_leader_allotype_info(hla_allotype))
            return jsonify(results)
        except Exception as e:
            return e.__dict__, 500


@ns_type.route("/genotype/<string:hla_genotype_input>")
class LeaderGenotype(Resource):
    def get(self, hla_genotype_input):
        """
        returns leader-peptide allotype(s) of HLA-B allele(s)
        """
        try:
            hla_genotypes = [
                geno.strip() for geno in list(set(hla_genotype_input.split(",")))
            ]
            results = []
            mapper = LeaderMapper()
            for hla_genotype in hla_genotypes:
                results.append(mapper.get_leader_genotype_info(hla_genotype))
            return jsonify(results)
        except Exception as e:
            return e.__dict__, 500


@ns_type.route("/map")
class LeaderMap(Resource):
    def get(self):
        """
        returns dictionary of HLA-B allotypes and corresponding leader types.
        """
        return jsonify(LeaderMapper().get_map())


@ns_match.route("/status")
class MatchStatus(Resource):

    model = api.model(
        "HLA-B Genotypes Input",
        {
            "hla-b_genotype_patient": fields.String(
                required=True,
                description="HLA-B genotype of the patient",
                help="HLA-B genotype format: B*XX:XX+B*YY:XX",
            ),
            "hla-b_genotype_donors": fields.String(
                required=True,
                description="HLA-B genotype of the donor",
                help="HLA-B genotype format: B*XX:XX+B*YY:XX",
            ),
        },
    )

    @api.expect(model)
    def post(self):
        """
        returns leader match status of single HLA-B-mismatched transplants sorted via a three-letter nomenclature: (1) non-shared patient's mismatch, (2) non-shared donor's mismatch, (3) shared allotype.
        """
        try:
            patient = request.json["hla-b_genotype_patient"]
            donors = request.json["hla-b_genotype_donors"]
            match = HlaBGenotypeMatch(
                HlaBGenotype(patient["genotype"], id=patient["id"]),
                [HlaBGenotype(donor["genotype"], id=donor["id"]) for donor in donors],
            )
            results = LeaderMapper().get_match_status_info(match)
            return jsonify(results)
        except Exception as e:
            return e.__dict__, 500


@app.after_request
def after_request(response):
    response.headers.add("Access-Control-Allow-Origin", "*")
    response.headers.add("Access-Control-Allow-Headers", "Content-Type,Authorization")
    response.headers.add("Access-Control-Allow-Methods", "GET,PUT,POST,DELETE")
    response.headers[
        "Strict-Transport-Security"
    ] = "max-age=31536000; includeSubDomains"
    response.headers["Content-Security-Policy"] = "default-src 'self' 'unsafe-inline'"
    response.headers["X-Content-Type-Options"] = "nosniff"
    response.headers["X-XSS-Protection"] = "1; mode=block"

    return response


if __name__ == "__main__":
    app.run("0.0.0.0", "5010", debug=True)