app.py

import sys

import io
import json
import requests
from rdflib import Graph
from flask import (
    Flask,
    Response,
    request,
    render_template,
    Markup,
    g,
    redirect,
    url_for,
)
from vocprez.model import *
from vocprez import _config as config
import vocprez.utils as u
from pyldapi import Renderer, ContainerRenderer
from vocprez.model import VocPrezRenderer, VocabulariesRenderer
import logging
import vocprez.source as source
import markdown
from flask_compress import Compress
from flaskext.markdown import Markdown

logging.basicConfig(
    filename=config.LOGFILE,
    level=logging.DEBUG,
    datefmt="%Y-%m-%d %H:%M:%S",
    format="%(asctime)s %(levelname)s %(filename)s:%(lineno)s %(message)s",
)

app = Flask(
    __name__, template_folder=config.TEMPLATES_DIR, static_folder=config.STATIC_DIR
)
app.config["COMPRESS_MIMETYPES"] = [
    'text/html',
    'text/css',
    'text/xml',
    'application/json',
    'application/geo+json',
    'application/javascript',
] + Renderer.RDF_MEDIA_TYPES
Compress(app)
Markdown(app)


# FUNCTION before_request
@app.before_request
def before_request():
    """
    Runs before every request and populates vocab index either from disk (VOCABS.p) or from a complete reload by
    calling collect() for each of the vocab sources defined in config/__init__.py -> VOCAB_SOURCES
    :return: nothing
    """
    logging.debug("before_request()")

    # always rebuild if DEBUG True
    if config.DEBUG:
        u.cache_reload()
    elif hasattr(g, "VOCABS"):
        # if g.VOCABS exists, if so, do nothing
        pass
    else:
        u.cache_load()
# END FUNCTION before_request


# FUNCTION context_processor
@app.context_processor
def context_processor():
    """
    A set of variables available globally for all Jinja templates.
    :return: A dictionary of variables
    :rtype: dict
    """
    return dict(
        utils=u,  # gives access to all functions defined in utils.py
    )
# END FUNCTION context_processor


# ROUTE index
@app.route("/")
def index():
    return VocPrezRenderer(
        request,
        config.SYSTEM_BASE_URI,
        config.VOCS_URI,
        config.VOCS_TITLE,
        config.VOCS_DESC,
        g.VOCABS
    ).render()
# END ROUTE index


# ROUTE vocabs
@app.route("/vocab/")
def vocabularies():
    return VocabulariesRenderer(
        request,
        g.VOCABS,
        config.SYSTEM_BASE_URI,
        config.VOCS_URI,
        config.VOCS_TITLE,
        config.VOCS_DESC
    ).render()
# END ROUTE vocabs


# ROUTE one vocab
@app.route("/vocab/<string:vocab_id>/")
def vocabulary(vocab_id):
    if vocab_id not in [x.id for x in g.VOCABS.values()]:
        return return_vocprez_error(
            "vocab_id not valid",
            400,
            markdown.markdown(
                "The 'vocab_id' you supplied, {}, is not known. Valid vocab_ids are:\n\n{}".format(
                    vocab_id,
                    "\n".join(
                        ["* [{}]({}): {}".format(x.id, u.get_content_uri(x.uri), x.title) for x in g.VOCABS.values()])
                )
            )
        )

    for v in g.VOCABS.values():
        if v.id == vocab_id:
            return redirect(url_for("object") + "?uri=" + v.uri)
# END ROUTE one vocab


# ROUTE concepts
@app.route("/vocab/<vocab_id>/concept/")
def concepts(vocab_id):
    if vocab_id not in [x.id for x in g.VOCABS.values()]:
        return return_vocprez_error(
            "vocab_id not valid",
            400,
            markdown.markdown(
                "The 'vocab_id' you supplied, {}, is not known. Valid vocab_ids are:\n\n{}".format(
                    vocab_id,
                    "\n".join(["* [{}]({}): {}".format(
                        x.id, u.get_content_uri(x.uri), x.title) for x in g.VOCABS.values()])
                )
            )
        )

    try:
        vocab_source = getattr(source, g.VOCABS[vocab_id].source)(vocab_id, request)
        cpts = vocab_source.list_concepts()
        # concepts.sort(key=lambda x: x["prefLabel"]) -- sort not needed when receiving pre-sorted tuples
        total = len(cpts)

        page = (
            int(request.values.get("page")) if request.values.get("page") is not None else 1
        )
        per_page = (
            int(request.values.get("per_page"))
            if request.values.get("per_page") is not None
            else 20
        )
        start = (page - 1) * per_page
        end = start + per_page
        members = cpts[start:end]
    except Exception as e:
        return Response(
            str(e),
            status=500,
            mimetype="text/plain"
        )

    return ContainerRenderer(
        request,
        url_for("concepts", vocab_id=vocab_id),
        "All Concepts",
        'All Concepts within Vocab {}'.format(vocab_id),
        None,
        None,
        members,
        total
    ).render()
# END ROUTE concepts


# ROUTE object
@app.route("/object")
def object():
    """
    This is the general RESTful endpoint and corresponding Python function to handle requests for individual objects,
    be they a Vocabulary (ConceptScheme), a Collection or Concept. Only those 3 classes of object are supported for the
    moment.

    An HTTP URI query string argument parameter 'uri' must be supplied, indicating the URI of the object being requested

    :return: A Flask Response object
    :rtype: :class:`flask.Response`
    """

    uri = request.values.get("uri")

    # must have a URI or Vocab URI supplied
    if uri is None:
        return return_vocprez_error(
            "Input Error",
            400,
            "A Query String Argument of 'uri' must be supplied for this endpoint"
        )

    if uri == config.SYSTEM_BASE_URI or uri == config.SYSTEM_BASE_URI + "/":
        return index()

    if uri == config.VOCS_URI or uri == config.VOCS_URI + "/":
        return vocabularies()

    # get the class of the object
    q = """
        PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

        SELECT DISTINCT ?c ?cs
        WHERE {
            GRAPH ?g {
                <xxx> a ?c .
                OPTIONAL {
                    VALUES ?memberof { skos:inScheme skos:topConceptOf }
                    <xxx> ?memberof ?cs .
                }
            }
        }
        """.replace("xxx", uri)
    cs = None
    for r in u.sparql_query(q):
        if r["c"]["value"] == "http://www.w3.org/2004/02/skos/core#ConceptScheme":
            if uri in g.VOCABS.keys():
                # get vocab details using appropriate source handler
                vocab = source.SPARQL(request).get_vocabulary(uri)
                return VocabularyRenderer(request, vocab).render()
            else:
                return None
        elif r["c"]["value"] == "http://www.w3.org/2004/02/skos/core#Collection":
            try:
                c = source.SPARQL(request).get_collection(uri)
                return CollectionRenderer(request, c).render()
            except:
                return None
        elif r["c"]["value"] == "http://www.w3.org/2004/02/skos/core#Concept":
            try:
                if r.get("cs"):
                    cs = r["cs"]["value"]
                c = source.SPARQL(request).get_concept(cs, uri)
                return ConceptRenderer(request, c).render()
            except:
                return None

    return return_vocprez_error(
        "Input Error",
        400,
        "The object with URI {} is not of type skos:ConceptScheme, skos:Collection or skos:Concept "
        "and only these classes of object are understood by VocPrez".format(uri)
    )
# END ROUTE object


# ROUTE about
@app.route("/about")
def about():
    import os

    # using basic Markdown method from http://flask.pocoo.org/snippets/19/
    with open(os.path.join(config.APP_DIR, "..", "README.md")) as f:
        content = f.read()

    # make images come from web dir
    content = content.replace(
        "vocprez/view/style/", request.url_root + "style/"
    )
    content = Markup(markdown.markdown(content, extensions=['tables']))

    return render_template(
        "about.html",
        title="About",
        navs={},
        content=content
    )
# END ROUTE about


# ROUTE sparql
@app.route("/sparql", methods=["GET", "POST"])
@app.route("/sparql/", methods=["GET", "POST"])
def sparql():
    # queries to /sparql with an accept header set to a SPARQL return type or an RDF type
    # are forwarded to /endpoint for a response
    # all others (i.e. with no Accept header, an Accept header HTML or for an unsupported Accept header
    # result in the SPARQL page HTML respose where the query is placed into the YasGUI UI for interactive querying
    SPARQL_RESPONSE_MEDIA_TYPES = [
        "application/sparql-results+json",
        "text/csv",
        "text/tab-separated-values",
    ]
    QUERY_RESPONSE_MEDIA_TYPES = ["text/html"] + SPARQL_RESPONSE_MEDIA_TYPES + Renderer.RDF_MEDIA_TYPES
    accept_type = request.accept_mimetypes.best_match(QUERY_RESPONSE_MEDIA_TYPES, "text/html")
    logging.debug("accept_type: " + accept_type)
    if accept_type in SPARQL_RESPONSE_MEDIA_TYPES or accept_type in Renderer.RDF_MEDIA_TYPES:
        # return data
        logging.debug("returning endpoint()")
        return endpoint()
    else:
        # return HTML UI
        logging.debug("returning sparql()")
        return render_template(
            "sparql.html",
        )
# END ROUTE sparql


# ROUTE search
@app.route("/search")
def search():
    if request.values.get("search"):
        last_search = request.values.get("search")
        if request.values.get("from") and request.values.get("from") != "all":
            grf = '<' + request.values.get("from") + '>'
            bind = f"BIND ({grf} AS ?g)"
        else:
            grf = "?g"
            bind = ""
        q = """
            PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

            SELECT DISTINCT ?g ?uri ?pl (SUM(?w) AS ?weight)
            WHERE {{                
                GRAPH {grf} {{
                    {{  # exact match on a prefLabel always wins
                        ?uri a skos:Concept ;
                             skos:prefLabel ?pl .
                        BIND (50 AS ?w)
                        FILTER REGEX(?pl, "^{input}$", "i")
                    }}
                    UNION    
                    {{
                        ?uri a skos:Concept ;
                             skos:prefLabel ?pl .
                        BIND (10 AS ?w)
                        FILTER REGEX(?pl, "{input}", "i")
                    }}
                    UNION
                    {{
                        ?uri a skos:Concept ;
                             skos:altLabel ?al ;
                             skos:prefLabel ?pl .
                        BIND (5 AS ?w)
                        FILTER REGEX(?al, "{input}", "i")
                    }}
                    UNION
                    {{
                        ?uri a skos:Concept ;
                             skos:hiddenLabel ?hl ;
                             skos:prefLabel ?pl .
                        BIND (5 AS ?w)
                        FILTER REGEX(?hl, "{input}", "i")
                    }}        
                    UNION
                    {{
                        ?uri a skos:Concept ;
                             skos:definition ?d ;
                             skos:prefLabel ?pl .
                        BIND (1 AS ?w)
                        FILTER REGEX(?d, "{input}", "i")
                    }}        
                }}
                
                {bind}
            }}
            GROUP BY ?g ?uri ?pl
            ORDER BY DESC(?weight) 
            """.format(**{"grf": grf, "input": request.values.get("search"), "bind": bind})
        results = {}

        for r in u.sparql_query(q):
            if r.get("uri") is None:
                break  # must do this check as r["weight"] will appear at least once with value 0 for no results

            if r["g"]["value"] not in results.keys():
                results[r["g"]["value"]] = []
            results[r["g"]["value"]].append((r["uri"]["value"], r["pl"]["value"]))

        return render_template(
            "search.html",
            vocabs=[(v.uri, v.title) for k, v in g.VOCABS.items()],
            last_search=last_search,
            selected_vocab=request.values.get("from"),
            results=results
        )
    else:
        return render_template(
            "search.html",
            vocabs=[(v.uri, v.title) for k, v in g.VOCABS.items()]
        )
# END ROUTE search


# ROUTE endpoint
# the SPARQL endpoint under-the-hood
@app.route("/endpoint", methods=["GET", "POST"])
def endpoint():
    """
    TESTS

    Form POST:
    curl -X POST -d query="PREFIX%20skos%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23%3E%0ASELECT%20* \
    %20WHERE%20%7B%3Fs%20a%20skos%3AConceptScheme%20.%7D" http://localhost:5000/endpoint

    Raw POST:
    curl -X POST -H 'Content-Type: application/sparql-query' --data-binary @query.sparql http://localhost:5000/endpoint
    using query.sparql:
        PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
        SELECT * WHERE {?s a skos:ConceptScheme .}

    GET:
    curl http://localhost:5000/endpoint?query=PREFIX%20skos%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore \
    %23%3E%0ASELECT%20*%20WHERE%20%7B%3Fs%20a%20skos%3AConceptScheme%20.%7D

    GET CONSTRUCT:
        PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
        PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
        CONSTRUCT {?s a rdf:Resource}
        WHERE {?s a skos:ConceptScheme}
    curl -H 'Accept: application/ld+json' http://localhost:5000/endpoint?query=PREFIX%20rdf%3A%20%3Chttp%3A%2F%2F \
    www.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0APREFIX%20skos%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2F \
    skos%2Fco23%3E%0ACONSTRUCT%20%7B%3Fs%20a%20rdf%3AResource%7D%0AWHERE%20%7B%3Fs%20a%20skos%3AConceptScheme%7D

    """
    logging.debug("request: {}".format(request.__dict__))

    def get_sparql_service_description(rdf_fmt="turtle"):
        """Return an RDF description of PROMS' read only SPARQL endpoint in a requested format

        :param rdf_fmt: 'turtle', 'n3', 'xml', 'json-ld'
        :return: string of RDF in the requested format
        """
        sd_ttl = """
            @prefix rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
            @prefix sd:     <http://www.w3.org/ns/sparql-service-description#> .
            @prefix sdf:    <http://www.w3.org/ns/formats/> .
            @prefix void:   <http://rdfs.org/ns/void#> .
            @prefix xsd:    <http://www.w3.org/2001/XMLSchema#> .

            <{0}>
                a                       sd:Service ;
                sd:endpoint             <{0}> ;
                sd:supportedLanguage    sd:SPARQL11Query ; # yes, read only, sorry!
                sd:resultFormat         sdf:SPARQL_Results_JSON ;  # yes, we only deliver JSON results, sorry!
                sd:feature sd:DereferencesURIs ;
                sd:defaultDataset [
                    a sd:Dataset ;
                    sd:defaultGraph [
                        a sd:Graph ;
                        void:triples "100"^^xsd:integer
                    ]
                ]
            .
        """.format(config.SYSTEM_BASE_URI + url_for("sparql"))
        grf = Graph().parse(io.StringIO(sd_ttl), format="turtle")
        rdf_formats = list(set([x for x in Renderer.RDF_SERIALIZER_TYPES_MAP]))
        if rdf_fmt in rdf_formats:
            return grf.serialize(format=rdf_fmt)
        else:
            raise ValueError(
                "Input parameter rdf_format must be one of: " + ", ".join(rdf_formats)
            )

    def sparql_query2(q, mimetype="application/json"):
        """ Make a SPARQL query"""
        logging.debug("sparql_query2: {}".format(q))
        data = q

        headers = {
            "Content-Type": "application/sparql-query",
            "Accept": mimetype,
            "Accept-Encoding": "UTF-8",
        }
        if config.SPARQL_USERNAME is not None and config.SPARQL_PASSWORD is not None:
            auth = (config.SPARQL_USERNAME, config.SPARQL_PASSWORD)
        else:
            auth = None

        try:
            logging.debug(
                "endpoint={}\ndata={}\nheaders={}".format(
                    config.SPARQL_ENDPOINT, data, headers
                )
            )
            if auth is not None:
                r = requests.post(
                    config.SPARQL_ENDPOINT, auth=auth, data=data, headers=headers, timeout=60
                )
            else:
                r = requests.post(
                    config.SPARQL_ENDPOINT, data=data, headers=headers, timeout=60
                )
            logging.debug("response: {}".format(r.__dict__))
            return r.content.decode("utf-8")
        except Exception as ex:
            raise ex

    format_mimetype = request.headers["ACCEPT"]

    # Query submitted
    if request.method == "POST":
        """Pass on the SPARQL query to the underlying endpoint defined in config
        """
        if "application/x-www-form-urlencoded" in request.content_type:
            """
            https://www.w3.org/TR/2013/REC-sparql11-protocol-20130321/#query-via-post-urlencoded

            2.1.2 query via POST with URL-encoded parameters

            Protocol clients may send protocol requests via the HTTP POST method by URL encoding the parameters. When
            using this method, clients must URL percent encode all parameters and include them as parameters within the
            request body via the application/x-www-form-urlencoded media type with the name given above. Parameters must
            be separated with the ampersand (&) character. Clients may include the parameters in any order. The content
            type header of the HTTP request must be set to application/x-www-form-urlencoded.
            """
            if (
                    request.values.get("query") is None
                    or len(request.values.get("query")) < 5
            ):
                return Response(
                    "Your POST request to the SPARQL endpoint must contain a 'query' parameter if form posting "
                    "is used.",
                    status=400,
                    mimetype="text/plain",
                )
            else:
                query = request.values.get("query")
        elif "application/sparql-query" in request.content_type:
            """
            https://www.w3.org/TR/2013/REC-sparql11-protocol-20130321/#query-via-post-direct

            2.1.3 query via POST directly

            Protocol clients may send protocol requests via the HTTP POST method by including the query directly and
            unencoded as the HTTP request message body. When using this approach, clients must include the SPARQL query
            string, unencoded, and nothing else as the message body of the request. Clients must set the content type
            header of the HTTP request to application/sparql-query. Clients may include the optional default-graph-uri
            and named-graph-uri parameters as HTTP query string parameters in the request URI. Note that UTF-8 is the
            only valid charset here.
            """
            query = request.data.decode("utf-8")  # get the raw request
            if query is None:
                return Response(
                    "Your POST request to this SPARQL endpoint must contain the query in plain text in the "
                    "POST body if the Content-Type 'application/sparql-query' is used.",
                    status=400,
                )
        else:
            return Response(
                "Your POST request to this SPARQL endpoint must either the 'application/x-www-form-urlencoded' or"
                "'application/sparql-query' ContentType.",
                status=400,
            )

        try:
            if "CONSTRUCT" in query:
                format_mimetype = "text/turtle"
                return Response(
                    sparql_query2(
                        query, mimetype=format_mimetype
                    ),
                    status=200,
                    mimetype=format_mimetype,
                )
            else:
                return Response(
                    sparql_query2(query, format_mimetype),
                    status=200,
                )
        except ValueError as e:
            return Response(
                "Input error for query {}.\n\nError message: {}".format(query, str(e)),
                status=400,
                mimetype="text/plain",
            )
        except ConnectionError as e:
            return Response(str(e), status=500)
    else:  # GET
        if request.args.get("query") is not None:
            # SPARQL GET request
            """
            https://www.w3.org/TR/2013/REC-sparql11-protocol-20130321/#query-via-get

            2.1.1 query via GET

            Protocol clients may send protocol requests via the HTTP GET method. When using the GET method, clients must
            URL percent encode all parameters and include them as query parameter strings with the names given above.

            HTTP query string parameters must be separated with the ampersand (&) character. Clients may include the
            query string parameters in any order.

            The HTTP request MUST NOT include a message body.
            """
            query = request.args.get("query")
            if "CONSTRUCT" in query:
                acceptable_mimes = [x for x in Renderer.RDF_MEDIA_TYPES]
                best = request.accept_mimetypes.best_match(acceptable_mimes)
                query_result = sparql_query2(
                    query, mimetype=best
                )
                file_ext = {
                    "text/turtle": "ttl",
                    "application/rdf+xml": "rdf",
                    "application/ld+json": "json",
                    "text/n3": "n3",
                    "application/n-triples": "nt",
                }
                return Response(
                    query_result,
                    status=200,
                    mimetype=best,
                    headers={
                        "Content-Disposition": "attachment; filename=query_result.{}".format(
                            file_ext[best]
                        )
                    },
                )
            else:
                query_result = sparql_query2(query)
                return Response(
                    query_result, status=200, mimetype="application/sparql-results+json"
                )
        else:
            # SPARQL Service Description
            """
            https://www.w3.org/TR/sparql11-service-description/#accessing

            SPARQL services made available via the SPARQL Protocol should return a service description document at the
            service endpoint when dereferenced using the HTTP GET operation without any query parameter strings
            provided. This service description must be made available in an RDF serialization, may be embedded in
            (X)HTML by way of RDFa, and should use content negotiation if available in other RDF representations.
            """

            acceptable_mimes = [x for x in Renderer.RDF_MEDIA_TYPES] + ["text/html"]
            best = request.accept_mimetypes.best_match(acceptable_mimes)
            if best == "text/html":
                # show the SPARQL query form
                return redirect(url_for("sparql"))
            elif best is not None:
                for item in Renderer.RDF_MEDIA_TYPES:
                    if item == best:
                        rdf_format = best
                        return Response(
                            get_sparql_service_description(
                                rdf_fmt=rdf_format
                            ),
                            status=200,
                            mimetype=best,
                        )

                return Response(
                    "Accept header must be one of " + ", ".join(acceptable_mimes) + ".",
                    status=400,
                )
            else:
                return Response(
                    "Accept header must be one of " + ", ".join(acceptable_mimes) + ".",
                    status=400,
                )
# END ROUTE endpoint


# FUNCTION return_vocrez_error
# TODO: allow conneg - at least text v. HTML
def return_vocprez_error(title, status, message):
    return render_template(
        "error.html",
        title=title,
        status=status,
        msg=message
    ), status
# END FUNCTION return_vocrez_error


# ROUTE cache_reload
@app.route("/cache-reload")
def cache_reload():
    u.cache_reload()

    return Response(
        "Cache reloaded",
        status=200,
        mimetype="text/plain"
    )
# END ROUTE cache_reload


# run the Flask app
if __name__ == "__main__":
    app.run(debug=config.DEBUG, threaded=True, port=config.PORT)