D-Net

#!/usr/bin/python

from flask import Flask, jsonify, request

from flask.json import JSONEncoder

from eu.dnetlib.es_connector import DLIESConnector

from flask_prometheus import monitor

from logger import dlilogger

DLI_INDEX = None

ES_HOST = None

def read_properies():

    f = open('api.properties')

    for line in f:

        s = line.strip().split('=')

        if s[0] == 'api.index':

            DLI_INDEX = s[1]

        if s[1] == 'es_index':

            ES_HOST = [x.strip() for x in s[1].split(',')]

class MyJSONEncoder(JSONEncoder):

    def default(self, obj):

        return obj.__dict__

app = Flask(__name__)

app.debug = False

app.json_encoder = MyJSONEncoder

base_dnet_url = "http://aggregator-dli.openaire.eu/dli/"

pid_resolver = {

    "pdb": "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s",

    "ncbi-n": "http://www.ncbi.nlm.nih.gov/gquery/?term=%s",

    "pmid": "http://www.ncbi.nlm.nih.gov/pubmed/%s",

    "pmcid": "http://www.ncbi.nlm.nih.gov/pmc/articles/%s",

    "pubmedid": "http://www.ncbi.nlm.nih.gov/pubmed/%s",

    "doi": "http://dx.doi.org/%s",

    "genbank": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "nuccore": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "swiss-prot": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "arrayexpress": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "biomodels": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "bmrb": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "ena": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "geo": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "ensembl": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "mgi": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "bind": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "pride": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "ddbj": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "bioproject": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "embl": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

    "sra": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",

}

class InvalidUsage(Exception):

    status_code = 400

    def __init__(self, message, status_code=None, payload=None):

        Exception.__init__(self)

        self.message = message

        if status_code is not None:

            self.status_code = status_code

        self.payload = payload

    def to_dict(self):

        rv = dict(self.payload or ())

        rv['message'] = self.message

        return rv

# Routes

@app.route('/')

def root():

    return app.send_static_file('index.html')

@app.route('/<path:path>')

def static_proxy(path):

    # send_static_file will guess the correct MIME type

    return app.send_static_file(path)

@app.route('/api/item/<path:identifier>', methods=['post', 'get'])

def get_item(identifier):

    if identifier:

        object_type = request.form.get('type')

        start = request.form.get('from')

        if object_type and len(object_type) == 0:

            object_type = None

        if start and len(start) == 0:

            start = None

        elif start:

            start = int(start)

        connector = DLIESConnector()

        return jsonify(result=connector.item_by_id(identifier, object_type, start))

    else:

        raise InvalidUsage('This view is gone', status_code=410)

@app.route('/api/stats/', methods=['post', 'get'])

def stats():

    raise Exception("Method to be implemented")

    # q = QueryResolver(host, base_dnet_url)

    # return jsonify(stats=q.get_stats())

@app.route('/api/ds_info/', methods=['post', 'get'])

def info():

    raise Exception("Method to be implemented")

@app.route('/api/stats_detail/', methods=['post', 'get'])

def stats_detail():

    return ""

@app.route('/api/resolveId', methods=['get'])

def resolveIdentifier():

    pid = request.form.get('pid')

    pid_type = request.form.get('pid_type')

    if pid_type!= None:

        if pid_type.lower() in  pid_resolver:

            return pid_resolver[pid_type.lower()] % pid

        elif pid_type.lower().strip() == 'url':

            return pid

        else:

            return "http://identifiers.org/%s:%s" % (pid_type, pid)

    return ""

@app.route('/api/queryPid/', methods=['post'])

def query_pid():

    if 'pid' in request.form:

        print "pid Request for %s "%request.form['pid']

    connector = DLIESConnector()

    result = connector.query_by_id(request.form['pid'])

    return jsonify(result=result)

@app.route('/api/post/', methods=['post', 'get'])

def query_post():

    action = None

    query = None

    filter_key = None

    result = {}

    start = 0

    if 'action' in request.form:

        action = request.form['action']

    if 'query' in request.form:

        query = request.form['query']

    if 'start' in request.form:

        start = 0

        try:

            start = int(request.form.get('start',0))

        except:

            pass

    if 'filter' in request.form:

        filter_key = request.form['filter']

    if action == 'query' and query is not None:

        connector = DLIESConnector()

        try:

            result = connector.simple_query(query, start=start, user_filter=filter_key)

        except Exception as e:

            print e

        return jsonify(result=result)

    else:

        return jsonify(error={'error_code': 'an error occur during query on server'})

if __name__ == '__main__':

    app.logger.addHandler(dlilogger)

    monitor(app, port=8000)

    app.run()

    # app.run(host="0.0.0.0")