reference_harvester_ws.py

from flask import Flask, jsonify, request
from utils import europe_pmc_api, mongo_access, config, nlp
from itertools import chain
from flask_cors import CORS

app = Flask(__name__)
CORS(app)


@app.route("/harvest/<int:pmid>", methods=["GET", "OPTIONS"])
def submit(pmid):
    use_alleles = request.args.get("useAlleles")
    alleles = None

    if use_alleles:
        with open(config.get("DEFAULT", "TARGET_ALLELE_FILE")) as f:
            alleles = f.read().splitlines()

    if mongo_access.exist(pmid):
        reference = mongo_access.get_by_pmid(pmid)
        scrub(reference)
        return jsonify(reference)

    reference = europe_pmc_api.get_paper_by_pmid(pmid)

    if reference is None:
        return jsonify({"error": "Error while trying to get data from EuropePMC"})

    reference = dict(
        chain(
            {
                "status": "pending",
                "alleles": [],
                "datasource": "manual",
                "consortiumPaper": False,
                "citations": [],
                "cites": [],
                "citedBy": [],
                "alleleCandidates": [],
                "comment": "",
                "tags": [],
            }.items(),
            reference.items(),
        )
    )
    reference["firstPublicationDate"] = str(
        reference["firstPublicationDate"].isoformat()
    )
    reference = nlp.get_fragments(reference, alleles)
    return reference


def scrub(obj, bad_key="_id"):
    if isinstance(obj, dict):
        for key in list(obj.keys()):
            if key == bad_key:
                del obj[key]
            else:
                scrub(obj[key], bad_key)
    elif isinstance(obj, list):
        for i in reversed(range(len(obj))):
            if obj[i] == bad_key:
                del obj[i]
            else:
                scrub(obj[i], bad_key)

    else:
        pass


if __name__ == "__main__":
    app.run(debug=True, port=8000, host="0.0.0.0")