test_api.py

from flask import Flask, Response, redirect, url_for, request, render_template
import random
import os
from rdflib import ConjunctiveGraph, Namespace
from pymongo import MongoClient
from bson import ObjectId
from bson.errors import InvalidId

from string import Template

from metrics.Evaluation import Evaluation

FC_spec = [
    {"id": "F1A", "category": "Findable", "label": "Unique IDs", "definition": ""},
    {"id": "F1B", "category": "Findable", "label": "Persistent IDs", "definition": ""},
    {
        "id": "F2A",
        "category": "Findable",
        "label": "Structured metadata",
        "definition": "",
    },
    {
        "id": "F2B",
        "category": "Findable",
        "label": "Shared vocabularies for metadata",
        "definition": "",
    },
    {
        "id": "A11",
        "category": "Accessible",
        "label": "Open resolution protocol",
        "definition": "",
    },
    {
        "id": "A12",
        "category": "Accessible",
        "label": "Authorisation procedure or access rights",
        "definition": "",
    },
    {
        "id": "I1",
        "category": "Interoperable",
        "label": "Machine readable format",
        "definition": "",
    },
    {
        "id": "I2",
        "category": "Interoperable",
        "label": "Use shared ontologies",
        "definition": "",
    },
    {
        "id": "I3",
        "category": "Interoperable",
        "label": "External links",
        "definition": "",
    },
    {
        "id": "R11",
        "category": "Reusable",
        "label": "Metadata includes license",
        "definition": "",
    },
    {
        "id": "R12",
        "category": "Reusable",
        "label": "Metadata includes provenance",
        "definition": "",
    },
    {
        "id": "R13",
        "category": "Reusable",
        "label": "Community standards",
        "definition": "",
    },
]

prefix = """
@prefix daq: <http://purl.org/eis/vocab/daq#> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix dqv: <http://www.w3.org/ns/dqv#> .
@prefix duv: <http://www.w3.org/ns/duv#> .
@prefix oa: <http://www.w3.org/ns/oa#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix sdmx-attribute: <http://purl.org/linked-data/sdmx/2009/attribute#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

@prefix : <https://fair-checker.france-bioinformatique.fr/data/> .
"""

FAIR_Checker_template = """
:$metric_id
    a dqv:Dimension ;
    skos:prefLabel "$metric_label"@en ;
    skos:definition "$metric_definition"@en ;
    dqv:inCategory :$category ."""

metrics_tpl = """
:$id
    a dqv:QualityMeasurement ;
    dqv:computedOn <$url> ;
    dqv:isMeasurementOf :$dimension ;
    dqv:value "$value"^^xsd:integer ;
    prov:generatedAtTime "$date"^^xsd:dateTime ;
    prov:wasAttributedTo <https://github.com/IFB-ElixirFr/fair-checker> ;
    rdfs:seeAlso <https://doi.org/10.1186/s13326-023-00289-5> ."""

app = Flask(__name__)


client = MongoClient()
db = client.fair_checker
evaluations = db.evaluations


@app.route("/data/<ID>")
def derefLD(ID):
    mimetype = None
    if "Content-Type" in request.headers:
        mimetype = request.headers["Content-Type"].split(";")[0]

    try:
        eval_json = evaluations.find_one({"_id": ObjectId(ID)})
        print(type(eval_json))
        print(eval_json)
        e = Evaluation()
        e.build_from_json(data=eval_json)
        ttl = e.to_rdf_turtle()
        kg = ConjunctiveGraph()
        try:
            kg.parse(data=ttl, format="turtle")
        except Exception:
            return Response(
                "Error while parsing RDF:\n\n" + e.to_rdf_turtle(), mimetype="text"
            )
        if mimetype == "application/json":
            return Response(kg.serialize(format="json-ld"), mimetype="application/json")
        elif mimetype == "application/ld+json":
            return Response(
                kg.serialize(format="json-ld"), mimetype="application/ld+json"
            )
        elif mimetype == "application/rdf+xml":
            return Response(kg.serialize(format="xml"), mimetype="application/rdf+xml")
        elif mimetype == "text/n3":
            return Response(kg.serialize(format="n3"), mimetype="text/n3")
        elif mimetype == "text/turtle":
            return Response(kg.serialize(format="turtle"), mimetype="text/turtle")
        else:
            return Response(kg.serialize(format="turtle"), mimetype="text/turtle")
    except InvalidId:
        return Response(f"Cannot find evaluation {ID}", mimetype="text")


if __name__ == "__main__":
    app.run(host="0.0.0.0", port=5000, debug=True)