processor.py

#!/usr/bin/env python3

import argparse
import datetime
import logging
import sys
import time
from contextlib import closing
from json import dumps

import requests
import yaml
from SPARQLWrapper import JSON, SPARQLWrapper

__author__ = "cjm"


def main():
    parser = argparse.ArgumentParser(
        description="Helper utils for OBO",
        formatter_class=argparse.RawTextHelpFormatter,
    )
    parser.add_argument(
        "-i", "--input", type=str, required=False, help="Input metadata file"
    )
    parser.add_argument(
        "-v",
        "--verbosity",
        default=0,
        action="count",
        help="Increase output verbosity (min.: 0, max. 2)",
    )
    subparsers = parser.add_subparsers(dest="subcommand", help="sub-command help")

    # SUBCOMMAND
    parser_n = subparsers.add_parser("check-urls", help="Ensure PURLs resolve")
    parser_n.set_defaults(function=check_urls)

    parser_n = subparsers.add_parser(
        "sparql-compare",
        help="Run SPARQL commands against the db to generate a " "consistency report",
    )
    parser_n.set_defaults(function=sparql_compare_all)

    parser_n = subparsers.add_parser("extract-context", help="Extracts JSON-LD context")
    parser_n.set_defaults(function=extract_context)

    parser_n = subparsers.add_parser(
        "extract-contributors",
        help="Queries github API for metadata about contributors",
    )
    parser_n.set_defaults(function=write_all_contributors)

    args = parser.parse_args()
    if args.verbosity >= 2:
        logging.basicConfig(level=logging.DEBUG)
    elif args.verbosity == 1:
        logging.basicConfig(level=logging.INFO)
    else:
        logging.basicConfig(level=logging.WARNING)

    with open(args.input, "r") as f:
        obj = yaml.load(f, Loader=yaml.SafeLoader)
        ontologies = obj["ontologies"]

    func = args.function
    func(ontologies, args)


def check_urls(ontologies, args):
    """
    Ensure PURLs resolve
    """

    def test_url(url):
        try:
            with closing(requests.get(url, stream=False)) as resp:
                return resp.status_code == 200
        except requests.exceptions.InvalidSchema as e:
            # TODO: requests lib doesn't handle ftp. For now simply return True in that case.
            if not format(e).startswith("No connection adapters were found for 'ftp:"):
                raise
            return True

    failed_ids = []
    for ont in ontologies:
        for p in ont.get("products", []):
            pid = p["id"]
            if not test_url(p.get("ontology_purl")):
                failed_ids.append(pid)
    if len(failed_ids) > 0:
        print("FAILURES:")
        for pid in failed_ids:
            print(pid, file=sys.stderr)
        exit(1)


def extract_context(ontologies, args):
    """
    Writes to STDOUT a sorted JSON map from ontology prefixes to PURLs
    """

    def has_obo_prefix(obj):
        return ("uri_prefix" not in obj) or (
            obj["uri_prefix"] == "http://purl.obolibrary.org/obo/"
        )

    prefix_map = {}
    for obj in ontologies:
        if has_obo_prefix(obj):
            prefix = obj.get("preferredPrefix") or obj["id"].upper()
            prefix_map[prefix] = {
                "@id": "http://purl.obolibrary.org/obo/" + prefix + "_",
                "@prefix": True,
            }

    print(
        dumps(
            {"@context": prefix_map}, sort_keys=True, indent=4, separators=(",", ": ")
        )
    )


def write_all_contributors(ontologies, args):
    """
    Query github API for all contributors to an ontology,
    write results as json
    """
    results = []
    for ont_obj in ontologies:
        id = ont_obj["id"]
        logging.info("Getting info for {}".format(id))
        repo_path = get_repo_path(ont_obj)
        if repo_path is not None:
            contribs = list(get_ontology_contributors(repo_path))
            print("CONTRIBS({})=={}".format(id, contribs))
            for c in contribs:
                print("#{}\t{}\n".format(id, c["login"]))
            results.append(dict(id=id, contributors=contribs))
        else:
            logging.warn("No repo_path declared for {}".format(id))
    print(dumps(results, sort_keys=True, indent=4, separators=(",", ": ")))


def get_ontology_contributors(repo_path):
    """
    Get individual contributors to a org/repo_path
    repo_path is a string "org/repo"
    """
    url = "https://api.github.com/repos/{}/contributors".format(repo_path)
    # TODO: allow use of oauth token;
    # GH has a quota for non-logged in API calls
    time.sleep(3)
    with closing(requests.get(url, stream=False)) as resp:
        ok = resp.status_code == 200
        if ok:
            results = resp.json()
            logging.info("RESP={}".format(results))
            return results
        else:
            logging.error("Failed: {}".format(url))
            return []


def get_repo_path(ont_obj):
    """
    Extract the repository path for the given object
    """
    repo_path = None
    if "repository" in ont_obj:
        repo_path = ont_obj["repository"]
    elif "tracker" in ont_obj:
        tracker = ont_obj["tracker"]
        if tracker is not None and "github" in tracker:
            repo_path = tracker.replace("/issues", "")

    if repo_path is not None:
        repo_path = repo_path.replace("https://github.com/", "")
        if repo_path.endswith("/"):
            repo_path = repo_path[:-1]
        return repo_path
    else:
        logging.warn("Could not get gh repo_path for ".format(ont_obj))
        return None


def run_sparql(obj, p, expected_value, q):
    """
    Generate a SPARQL statement using query q and parameter p, and expect 'expected_value' as the
    result. Print out a message indicating whether the there is or is not a match for the given object
    """
    sparql = SPARQLWrapper("http://sparql.hegroup.org/sparql")
    sparql.setQuery(q)
    sparql.setReturnFormat(JSON)
    results = sparql.query().convert()

    id = obj["id"]
    got_value = False
    is_match = False
    vs = []

    for result in results["results"]["bindings"]:
        got_value = True
        v = result[p]["value"]
        vs.append(str(v))
        if v == expected_value:
            is_match = True

    if got_value and is_match:
        msg = "CONSISTENT"
    elif got_value and not is_match:
        if expected_value == "":
            msg = "UNDECLARED_LOCAL: REMOTE:" + ",".join(vs)
        else:
            msg = "INCONSISTENT: REMOTE:" + ",".join(vs) + " != LOCAL:" + expected_value
    else:
        msg = "UNDECLARED_REMOTE"
    print(id + " " + p + " " + msg)


def sparql_compare_ont(obj):
    """
    Some ontologies will directly declare some subset of the OBO metadata
    directly in the ontology header. In the majority of cases we should
    yield to the provider. However, we reserve the right to override. For
    example, OBO may have particular guidelines about the length of the title,
    required for coherency within the registry. All differences should be
    discussed with the provider and an accomodation reached
    """
    if "ontology_purl" not in obj:
        return

    purl = obj["ontology_purl"]
    # this could be made more declarative, or driven by the context.jsonld mapping;
    # however, for now this is relatively simple and easy to understand:
    run_sparql(
        obj,
        "license",
        obj["license"]["url"] if "license" in obj else "",
        "SELECT DISTINCT ?license WHERE {<"
        + purl
        + "> <http://purl.org/dc/elements/1.1/license> ?license}",
    )
    run_sparql(
        obj,
        "title",
        obj["title"] if "title" in obj else "",
        "SELECT DISTINCT ?title WHERE {<"
        + purl
        + "> <http://purl.org/dc/elements/1.1/title> ?title}",
    )
    run_sparql(
        obj,
        "description",
        obj["description"] if "description" in obj else "",
        "SELECT DISTINCT ?description WHERE {<"
        + purl
        + "> <http://purl.org/dc/elements/1.1/description> ?description}",
    )
    run_sparql(
        obj,
        "homepage",
        obj["homepage"] if "homepage" in obj else "",
        "SELECT DISTINCT ?homepage WHERE {<"
        + purl
        + "> <http://xmlns.com/foaf/0.1/homepage> ?homepage}",
    )


def sparql_compare_all(ontologies, args):
    """
    Run sparql_compare_ont() on all the given ontologies.
    """
    # The `args` parameter is not used here but it is convenient to have it in our definition, since
    # whether this function or one of the other main `subcommands` of this script is called is
    # determine dynamically, and we want all of the subcommands to have a consistent signature.
    for obj in ontologies:
        sparql_compare_ont(obj)


if __name__ == "__main__":
    main()