import atexit
import base64

from app.metrics.pennsieve import get_download_count
from app.metrics.contentful import init_cf_cda_client, get_funded_projects_count, get_featured_datasets
from scripts.update_contentful_entries import update_all_events_sort_order, update_event_sort_order
from app.metrics.algolia import get_dataset_count, init_algolia_client, get_all_dataset_ids, get_associated_datasets
from app.metrics.ga import init_ga_reporting, get_ga_1year_sessions
from scripts.monthly_stats import MonthlyStats
from scripts.update_featured_dataset_id import set_featured_dataset_id, get_featured_dataset_id_table_state
from app.osparc.services import OSparcServices

import botocore
import boto3
import json
import logging
import re
import requests
from urllib.parse import urlparse

from apscheduler.schedulers.background import BackgroundScheduler
from apscheduler.triggers.combining import OrTrigger
from apscheduler.triggers.date import DateTrigger
from apscheduler.triggers.interval import IntervalTrigger
from botocore.exceptions import ClientError
from datetime import datetime, timedelta
from flask import Flask, abort, jsonify, request
from flask_cors import CORS
from flask_marshmallow import Marshmallow
from pennsieve import Pennsieve
from pennsieve.base import UnauthorizedException as PSUnauthorizedException
from PIL import Image
from requests.auth import HTTPBasicAuth
from flask_caching import Cache

from app.scicrunch_requests import create_doi_query, create_filter_request, create_facet_query, create_doi_aggregate, create_title_query, \
    create_identifier_query, create_pennsieve_identifier_query, create_field_query, create_request_body_for_curies, create_onto_term_query, \
    create_multiple_doi_query, create_multiple_discoverId_query, create_anatomy_query, get_body_scaffold_dataset_id, \
    create_multiple_mimetype_query
from scripts.email_sender import EmailSender, feedback_email, general_interest_email, issue_reporting_email, creation_request_confirmation_email, service_interest_email
from threading import Lock
from xml.etree import ElementTree

from app.config import Config
from app.dbtable import MapTable, ScaffoldTable, FeaturedDatasetIdSelectorTable
from app.scicrunch_process_results import process_results, process_get_first_scaffold_info, reform_aggregation_results, \
    reform_curies_results, reform_dataset_results, reform_related_terms, reform_anatomy_results
from app.serializer import ContactRequestSchema
from app.utilities import img_to_base64_str, get_path_from_mangled_list
from app.osparc.osparc import start_simulation as do_start_simulation
from app.osparc.osparc import check_simulation as do_check_simulation
from app.biolucida_process_results import process_results as process_biolucida_results, process_result as process_biolucida_result

logging.basicConfig()

app = Flask(__name__)
# set environment variable
app.config["ENV"] = Config.DEPLOY_ENV
cache = Cache(app, config={'CACHE_TYPE': 'SimpleCache', 'CACHE_DEFAULT_TIMEOUT': 300})

CORS(app)

ma = Marshmallow(app)
email_sender = EmailSender()

ps = None
s3 = boto3.client(
    "s3",
    aws_access_key_id=Config.SPARC_PORTAL_AWS_KEY,
    aws_secret_access_key=Config.SPARC_PORTAL_AWS_SECRET,
    region_name="us-east-1",
)

biolucida_lock = Lock()

try:
    maptable = MapTable(Config.DATABASE_URL)
except AttributeError:
    maptable = None

try:
    scaffoldtable = ScaffoldTable(Config.DATABASE_URL)
except AttributeError:
    scaffoldtable = None

try:
    featuredDatasetIdSelectorTable = FeaturedDatasetIdSelectorTable(Config.DATABASE_URL)
except AttributeError:
    featuredDatasetIdSelectorTable = None


class Biolucida(object):
    _token = ''
    _expiry_date = datetime.now() + timedelta(999999)
    _pending_authentication = False

    @staticmethod
    def set_token(value):
        Biolucida._token = value

    def token(self):
        return self._token

    @staticmethod
    def set_expiry_date(value):
        Biolucida._expiry_date = value

    def expiry_date(self):
        return self._expiry_date

    @staticmethod
    def set_pending_authentication(value):
        Biolucida._pending_authentication = value

    def pending_authentication(self):
        return self._pending_authentication


@app.errorhandler(404)
def resource_not_found(e):
    return jsonify(error=str(e)), 404


@app.before_first_request
def connect_to_pennsieve():
    global ps
    try:
        ps = Pennsieve(
            api_token=Config.PENNSIEVE_API_TOKEN,
            api_secret=Config.PENNSIEVE_API_SECRET,
            env_override=False,
            host=Config.PENNSIEVE_API_HOST
        )
    except requests.exceptions.HTTPError as err:
        logging.error("Unable to connect to Pennsieve host")
        logging.error(err)
    except PSUnauthorizedException as err:
        logging.error("Unable to authorise with Pennsieve Api")
        logging.error(err)
    except Exception as err:
        logging.error("Unknown Error")
        logging.error(err)


viewers_scheduler = BackgroundScheduler()
metrics_scheduler = BackgroundScheduler()
services_scheduler = BackgroundScheduler()
featured_dataset_id_scheduler = BackgroundScheduler()
update_contentful_event_entries_scheduler = BackgroundScheduler()

if not featured_dataset_id_scheduler.running:
    logging.info('Starting scheduler for featured dataset id acquisition')
    featured_dataset_id_scheduler.start()

# Run monthly stats email schedule on production
if Config.DEPLOY_ENV == 'production':
    monthly_stats_email_scheduler = BackgroundScheduler()
    ms = MonthlyStats()
    #Check when app starts in case the api server is down on the first
    #of the month
    ms.monthly_stats_required_check()
    monthly_stats_email_scheduler.start()
    #Check on the first of each month at 2am
    monthly_stats_email_scheduler.add_job(ms.monthly_stats_required_check, 'cron', \
        year='*', month='*', day='1', hour='2', minute=0, second=0)


# Only need to run the update contentful entries scheduler on one environment, so dev was chosen to keep prod more responsive
if Config.DEPLOY_ENV == 'development' and Config.SPARC_API_DEBUGGING == 'FALSE':
    if not update_contentful_event_entries_scheduler.running:
        logging.info('Starting scheduler for updating contentful event entries')
        update_contentful_event_entries_scheduler.start()
    # Update the contentful entries daily at 2 AM EST
    update_contentful_event_entries_scheduler.add_job(update_all_events_sort_order, 'cron', hour=2, timezone='US/Eastern')


osparc_data = {}

@app.before_first_request
def get_osparc_file_viewers():
    logging.info('Getting oSPARC viewers')
    # Gets a list of default viewers.
    try:
        req = requests.get(url=f'{Config.OSPARC_API_HOST}/viewers')
        if req.ok and 'application/json' in req.headers.get('content-type', ''):
            viewers = req.json()
            table = build_filetypes_table(viewers["data"])
            osparc_data["file_viewers"] = table
    except Exception as e:
        logging.error('Could not retreive oSPARC viewers', e)
    if not viewers_scheduler.running:
        logging.info('Starting scheduler for oSPARC viewers acquisition')
        viewers_scheduler.start()


usage_metrics = {}
google_analytics = init_ga_reporting()
algolia = init_algolia_client()
contentful = init_cf_cda_client()


@app.before_first_request
def get_metrics():
    logging.info('Gathering metrics data')

    if google_analytics:
        ga_response = get_ga_1year_sessions(google_analytics)
        usage_metrics['1year_sessions_count'] = ga_response

    if algolia:
        algolia_response = get_dataset_count(algolia)
        usage_metrics['dataset_count'] = algolia_response

    if contentful:
        cf_response = get_funded_projects_count(contentful)
        usage_metrics['funded_projects_count'] = cf_response

    ps_response = get_download_count()
    usage_metrics['1year_download_count'] = ps_response

    if not metrics_scheduler.running:
        logging.info('Starting scheduler for metrics acquisition')
        metrics_scheduler.start()

osparc_services = OSparcServices()

@app.before_first_request
def get_services():
    logging.info('Fetching oSPARC services')
    try:
        req = requests.get(url=f'{Config.OSPARC_API_HOST}/services')
        services_resp = req.json()
        osparc_services.set_services(services_resp['data'])
    except Exception as e:
        logging.error('Request to get oSPARC services failed', e)


# Gets oSPARC services before the first request after startup and then once a day.
services_scheduler.add_job(func=get_services, trigger="interval", days=1)

# Gets oSPARC viewers before the first request after startup and then once a day.
viewers_scheduler.add_job(func=get_osparc_file_viewers, trigger="interval", days=1)

# Gathers all the required metrics, once every three hours
metrics_scheduler.add_job(func=get_metrics, trigger='interval', hours=3)

# Update the featured dataset id on deploy and then every hour
featured_dataset_id_trigger = OrTrigger([DateTrigger(), IntervalTrigger(hours=1)])
featured_dataset_id_scheduler.add_job(lambda: set_featured_dataset_id(featuredDatasetIdSelectorTable), featured_dataset_id_trigger)

def shutdown_schedulers():
    logging.info('Stopping scheduler for oSPARC viewers acquisition')
    if viewers_scheduler.running:
        viewers_scheduler.shutdown()
    logging.info('Stopping scheduler for metrics acquisition')
    if metrics_scheduler.running:
        metrics_scheduler.shutdown()
    logging.info('Stopping scheduler for updating contentful entries')
    if update_contentful_event_entries_scheduler.running:
        update_contentful_event_entries_scheduler.shutdown()
    logging.info('Stopping scheduler for updating featured dataset id')
    if featured_dataset_id_scheduler.running:
        featured_dataset_id_scheduler.shutdown()
    logging.info('Stopping scheduler for oSPARC services')
    if services_scheduler.running:
        services_scheduler.shutdown()


atexit.register(shutdown_schedulers)


@app.route("/health")
def health():
    return json.dumps({"status": "healthy"})


@app.route("/contact", methods=["POST"])
def contact():
    data = json.loads(request.data)
    contact_request = ContactRequestSchema().load(data)

    name = contact_request["name"]
    email = contact_request["email"]
    message = contact_request["message"]

    email_sender.send_email(name, email, message)
    email_sender.sendgrid_email(Config.SES_SENDER, email, 'Feedback submission', feedback_email.substitute({ 'message': message }))

    return json.dumps({"status": "sent"})

def create_s3_presigned_url(s3BucketName, key, content_type, expiration):
    response = s3.generate_presigned_url(
        "get_object",
        Params={"Bucket": s3BucketName, "Key": key, "RequestPayer": "requester", "ResponseContentType": content_type},
        ExpiresIn=expiration,
    )

    return response


# Download a file from S3
@app.route("/download")
def create_presigned_url(expiration=3600, bucket_name=Config.DEFAULT_S3_BUCKET_NAME):
    key = request.args.get("key")
    s3BucketName = request.args.get("s3BucketName", bucket_name)
    content_type = request.args.get("contentType", "application/octet-stream")

    return create_s3_presigned_url(s3BucketName, key, content_type, expiration)


@app.route("/thumbnail/neurolucida")
def thumbnail_from_neurolucida_file():
    query_args = request.args
    if 'version' not in query_args or 'datasetId' not in query_args or 'path' not in query_args:
        return abort(400, description=f"Query arguments are not valid.")

    url = f"{Config.NEUROLUCIDA_HOST}/thumbnail"
    try:    
        response = requests.get(url, params=query_args, timeout=5)
        response.raise_for_status()
        if response.status_code == 200:
            if response.headers.get('Content-Type', 'unknown') == 'image/png':
                return base64.b64encode(response.content)
        abort(400, 'Failed to retrieve thumbnail.')
    
    except requests.exceptions.ConnectionError:
        return abort(400, description="Unable to make a connection to NEUROLUCIDA_HOST.")
    except requests.exceptions.Timeout:
        return abort(504, 'Request to NEUROLUCIDA_HOST timed out.')
    except requests.exceptions.RequestException as e:
        return abort(502, f"Error while requesting NEUROLUCIDA_HOST: {str(e)}")


@app.route("/thumbnail/segmentation")
def extract_thumbnail_from_xml_file(bucket_name=Config.DEFAULT_S3_BUCKET_NAME):
    """
    Extract a thumbnail from a mbf xml file.
    First phase is to find the thumbnail element in the xml document.
    Second phase is to convert the xml to a base64 png.
    """
    query_args = request.args
    if 'path' not in query_args:
        return abort(400, description=f"Query arguments are not valid.")

    s3BucketName = query_args.get("s3BucketName", bucket_name)
    path = query_args['path']
    resource = None
    start_tag_found = False
    end_tag_found = False
    start_byte = 0
    offset = 256000
    end_byte = offset
    while not start_tag_found or not end_tag_found:
        try:
            response = s3.get_object(
                Bucket=s3BucketName,
                Key=path,
                Range=f"bytes={start_byte}-{end_byte}",
                RequestPayer="requester"
            )
        except ClientError as ex:
            if ex.response['Error']['Code'] == 'NoSuchKey':
                return abort(404, description=f"Could not find file: '{path}'")
            else:
                return abort(404, description=f"Unknown error for file: '{path}'")

        resource = response["Body"].read().decode('UTF-8')
        start_tag_found = '<thumbnail ' in resource
        end_tag_found = '</thumbnail>' in resource
        if start_tag_found and not end_tag_found:
            end_byte += offset
        else:
            start_byte += offset
            end_byte += offset

        if len(resource) < offset:
            return abort(404, description=f"Could not find thumbnail in file: '{path}'")

    if resource is None:
        return abort(404, description=f"Could not find thumbnail in file: '{path}'")

    start_thumbnail_element = resource[resource.find('<thumbnail '):]
    thumbnail_xml = start_thumbnail_element[:start_thumbnail_element.find('</thumbnail>')] + '</thumbnail>'
    xml = ElementTree.fromstring(thumbnail_xml)
    size_info = xml.attrib
    im_data = ''
    for child in xml:
        im_data += child.text[2:]

    byte_im_data = bytes.fromhex(im_data)
    im = Image.frombytes("RGB", (int(size_info['rows']), int(size_info['cols'])), byte_im_data)
    base64_form = img_to_base64_str(im)

    return base64_form


@app.route("/exists/<path:path>")
def url_exists(path, bucket_name=Config.DEFAULT_S3_BUCKET_NAME):

    query_args = request.args
    s3BucketName = query_args.get("s3BucketName", bucket_name)

    try:
        head_response = s3.head_object(
            Bucket=s3BucketName,
            Key=path,
            RequestPayer="requester"
        )
    except ClientError:
        return {'exists': 'false'}

    content_length = head_response.get('ContentLength', 0)

    if content_length > 0:
        return {'exists': 'true'}

    return {'exists': 'false'}


def fetch_discover_file_information(uri):
    # Fudge the URI from Sci-crunch
    uri = uri.replace('https://api.pennsieve.io/', 'https://api.pennsieve.io/discover/')
    uri = uri[:uri.rfind('/')]

    r = requests.get(uri)
    return r.json()


@app.route("/s3-resource/discover_path")
def get_discover_path():
    uri = request.args.get('uri')

    try:
        json_response = fetch_discover_file_information(uri)
        if 'totalCount' in json_response and json_response['totalCount'] == 1:
            file_info = json_response['files'][0]
            return file_info['path']
    except Exception as ex:
        logging.error('Failed to retrieve uri {uri}', ex)
    return abort(404, description=f'Failed to retrieve uri {uri}')

def s3_header_check(path, bucket_name):
    try:
        head_response = s3.head_object(
            Bucket=bucket_name,
            Key=path,
            RequestPayer="requester"
        )
        content_length = head_response.get('ContentLength', Config.DIRECT_DOWNLOAD_LIMIT)
        if content_length and not content_length < Config.DIRECT_DOWNLOAD_LIMIT :  # 20 MB
            return abort(413, description= f"File too big to download: {content_length}")
    except botocore.exceptions.ClientError as err:
        # NOTE: This case is required because of https://github.com/boto/boto3/issues/2442
        if err.response["Error"]["Code"] == "404":
            return (404, f'Provided path was not found on the s3 resource')
        elif err.response["Error"]["Code"] == "403":
            return (403, f'There is a permission issue when accessing the file at specified path')
        else:
            return abort(err.response["Error"]["Code"], err.response["Error"]["Message"])
    else:
        return (200, 'OK')

# Reverse proxy for objects from S3, a simple get object
# operation. This is used by scaffoldvuer and its
# important to keep the relative <path> for accessing
# other required files.
@app.route("/s3-resource/<path:path>")
def direct_download_url(path, bucket_name=Config.DEFAULT_S3_BUCKET_NAME):

    query_args = request.args
    s3BucketName = query_args.get("s3BucketName", bucket_name)
    s3_path = path  # Will modify s3_path if we find name mangling

    # Check the header to see if too large or does not exist
    response = s3_header_check(path, s3BucketName)

    # If the file does not exist, check if the name was mangled
    if response[0] == 404 or response[0] == 403:
        s3_path_modified = get_path_from_mangled_list(path)
        if s3_path_modified == s3_path:
            abort(404, description=f'Provided path was not found on the s3 resource')  # Abort if path did not change

        # Check the modified path
        response2 = s3_header_check(s3_path_modified, s3BucketName)
        if response2[0] == 200:
            s3_path = s3_path_modified  # Modify the path if de-mangling was successful
        elif response2[0] == 404:
            abort(404, description=f'Provided path was not found on the s3 resource')
        elif response2[0] == 403:
            abort(403, description=f'There is a permission issue when accessing the file at specified path')


    response = s3.get_object(
        Bucket=s3BucketName,
        Key=s3_path,
        RequestPayer="requester"
    )

    encode_base64 = request.args.get("encodeBase64")
    resource = response["Body"].read()
    if encode_base64 is not None:
        return base64.b64encode(resource)

    return resource


@app.route("/scicrunch-dataset/<doi1>/<doi2>")
def sci_doi(doi1, doi2):
    doi = doi1.replace('DOI:', '') + '/' + doi2
    data = create_doi_query(doi)

    try:
        response = requests.post(
            f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
            json=data)
        return response.json()
    except requests.exceptions.HTTPError as err:
        logging.error(err)
        return json.dumps({'error': err})


# /pubmed/<id> Used as a proxy for making requests to pubmed
@app.route("/pubmed/<id_>")
@app.route("/pubmed/<id_>/")
def pubmed(id_):
    try:
        response = requests.get(f'https://pubmed.ncbi.nlm.nih.gov/{id_}/')
        return response.text
    except requests.exceptions.HTTPError as err:
        logging.error(err)
        return json.dumps({'error': err})


# /scicrunch-query-string/: Returns results for given organ curie. These can be processed by the sidebar
@app.route("/scicrunch-query-string/")
def sci_organ():
    fields = request.args.getlist('field')
    curie = request.args.get('curie')
    size = request.args.get('size')
    from_ = request.args.get('from')

    data = create_field_query(fields, curie, size, from_)

    try:
        response = requests.post(
            f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
            json=data)
        return process_results(response.json())
    except requests.exceptions.HTTPError as err:
        logging.error(err)
        return json.dumps({'error': err})


@app.route("/dataset_info/using_doi")
def get_dataset_info_doi():
    doi = request.args.get('doi')
    raw = request.args.get('raw_response')
    query = create_doi_query(doi)

    if raw is None:
        return reform_dataset_results(dataset_search(query))

    return dataset_search(query)

@app.route("/dataset_info/using_multiple_dois")
@app.route("/dataset_info/using_multiple_dois/")
def get_dataset_info_dois():
    dois = request.args.getlist('dois')
    query = create_multiple_doi_query(dois)

    return process_results(dataset_search(query))

@app.route("/multiple_dataset_info/using_multiple_mimetype")
@app.route("/multiple_dataset_info/using_multiple_mimetype/")
def get_file_info_from_mimetype():
    # q here is a scicrunch query ie: "*jp2*+OR+*vnd.ome.xml*+OR+*jpx*"
    q = request.args.getlist('q')
    query = create_multiple_mimetype_query(q)

    return process_results(dataset_search(query))


@app.route("/dataset_info/using_multiple_discoverIds")
@app.route("/dataset_info/using_multiple_discoverIds/")
def get_dataset_info_discoverIds():
    discoverIds = request.args.getlist('discoverIds')
    query = create_multiple_discoverId_query(discoverIds)

    return process_results(dataset_search(query))


@app.route("/dataset_info/using_title")
def get_dataset_info_title():
    title = request.args.get('title')
    query = create_title_query(title)

    return reform_dataset_results(dataset_search(query))


@app.route("/dataset_info/using_object_identifier")
def get_dataset_info_object_identifier():
    identifier = request.args.get('identifier')
    query = create_identifier_query(identifier)

    return reform_dataset_results(dataset_search(query))


@app.route("/dataset_info/anatomy")
def get_dataset_info_anatomy():
    identifier = request.args.get('identifier', -1)
    if identifier == -1:
        return abort(404, description=f'Identifier for API call not set.')

    query = create_anatomy_query(identifier)

    return reform_anatomy_results(dataset_search(query))


@app.route("/dataset_info/using_pennsieve_identifier")
def get_dataset_info_pennsieve_identifier():
    identifier = request.args.get('identifier')
    query = create_pennsieve_identifier_query(identifier)

    return reform_dataset_results(dataset_search(query))


@app.route("/segmentation_info/")
def get_segmentation_info_from_file(bucket_name=Config.DEFAULT_S3_BUCKET_NAME):
    query_args = request.args

    if 'dataset_path' not in query_args:
        return abort(400, description=f"Query arguments must include 'dataset_path'.")

    s3BucketName = query_args.get("s3BucketName", bucket_name)
    dataset_path = query_args.get('dataset_path')

    try:
        # Check the header to see if too large
        response = s3_header_check(dataset_path, s3BucketName)
        # Check if file exists
        if response[0] == 404:
            abort(404, description=f'Provided path was not found on the s3 resource')
        response = s3.get_object(
            Bucket=s3BucketName,
            Key=dataset_path,
            RequestPayer="requester"
        )
    except ClientError as ex:
        if ex.response['Error']['Code'] == 'NoSuchKey':
            return abort(404, description=f"Could not find file: '{dataset_path}'")
        else:
            return abort(404, description=f"Unknown error for file: '{dataset_path}'")

    resource = response["Body"].read()
    xml = ElementTree.fromstring(resource)
    subject_element = xml.find('./{*}sparcdata/{*}subject')
    info = {}
    if subject_element is not None:
        info['subject'] = subject_element.attrib
    else:
        info['subject'] = {'age': '', 'sex': '', 'species': '', 'subjectid': ''}

    atlas_element = xml.find('./{*}sparcdata/{*}atlas')
    if atlas_element is not None:
        info['atlas'] = atlas_element.attrib
    else:
        info['atlas'] = {'organ': ''}

    return info


@app.route("/current_doi_list")
def get_all_doi():
    query = create_doi_aggregate()
    results = reform_aggregation_results(dataset_search(query))
    doi_results = []
    for result in results['doi']['buckets']:
        doi_results.append(result['key']['curie'])

    return {'results': doi_results}


def dataset_search(query):
    try:
        payload = query

        params = {
            "api_key": Config.KNOWLEDGEBASE_KEY
        }
        response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
                                 json=payload, params=params)

        return response.json()
    except requests.exceptions.HTTPError as err:
        logging.error(err)

        return jsonify({'error': err})


# /search/: Returns sci-crunch results for a given <search> query
@app.route("/search/", defaults={'query': '', 'limit': 10, 'start': 0})
@app.route("/search/<query>")
def kb_search(query, limit=10, start=0):
    try:
        if request.args.get('limit') is not None:
            limit = request.args.get('limit')
        if request.args.get('query') is not None:
            query = request.args.get('query')
        if request.args.get('start') is not None:
            start = request.args.get('start')

        # print(f'{Config.SCI_CRUNCH_HOST}/_search?q={query}&size={limit}&from={start}&api_key={Config.KNOWLEDGEBASE_KEY}')
        response = requests.get(f'{Config.SCI_CRUNCH_HOST}/_search?q={query}&size={limit}&from={start}&api_key={Config.KNOWLEDGEBASE_KEY}')
        return process_results(response.json())
    except requests.exceptions.HTTPError as err:
        logging.error(err)
        return json.dumps({'error': err})


# /filter-search/: Returns sci-crunch results with optional params for facet filtering, sizing, and pagination
@app.route("/filter-search/", defaults={'query': ''})
@app.route("/filter-search/<query>/")
def filter_search(query):
    terms = request.args.getlist('term')
    facets = request.args.getlist('facet')
    size = request.args.get('size')
    start = request.args.get('start')

    # Create request
    data = create_filter_request(query, terms, facets, size, start)

    # Send request to sci-crunch
    try:
        response = requests.post(
            f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
            json=data)
        results = process_results(response.json())
    except requests.exceptions.HTTPError as err:
        logging.error(err)
        return jsonify({'error': str(err), 'message': 'SciCrunch is not currently reachable, please try again later'}), 502
    except json.JSONDecodeError:
        return jsonify({'message': 'Could not parse SciCrunch output, please try again later',
                        'error': 'JSONDecodeError'}), 502
    return results


# /get-facets/: Returns available sci-crunch facets for filtering over given a <type> ('species', 'gender' etc)
@app.route("/get-facets/<type_>")
def get_facets(type_):
    # Create facet query
    type_map, data = create_facet_query(type_)

    # Make a request for each sci-crunch parameter
    results = []
    for path in type_map[type_]:
        data['aggregations'][f'{type_}']['terms']['field'] = path
        try:
            response = requests.post(
                f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
                json=data)
            json_result = response.json()
            results.append(json_result)
        except json.JSONDecodeError:
            return jsonify({'message': 'Could not parse SciCrunch output, please try again later',
                            'error': 'JSONDecodeError'}), 502
        except Exception as ex:
            logging.error(f"Could not search SciCrunch for path {path}", ex)


    # Select terms from the results
    terms = []
    for result in results:
        terms += result['aggregations'][f'{type_}']['buckets']

    return jsonify(terms)


def inject_markdown(resp):
    if "readme" in resp:
        mark_req = requests.get(resp.get("readme"))
        resp["markdown"] = mark_req.text


def inject_template_data(resp):
    id_ = resp.get("id")
    uri = resp.get("uri")
    if id_ is None or uri is None:
        return
    parsed_uri = urlparse(uri)
    bucket = parsed_uri.netloc
    try:
        response = s3.get_object(
            Bucket=bucket,
            Key="{}/files/template.json".format(id_),
            RequestPayer="requester",
        )
    except ClientError:
        # If the file is not under folder 'files', check under folder 'packages'
        debugging = Config.SPARC_API_DEBUGGING == "TRUE"
        if debugging:
            logging.warning(
                "Required file template.json was not found under /files folder, trying under /packages..."
            )
        try:
            response = s3.get_object(
                Bucket=bucket,
                Key="{}/packages/template.json".format(id_),
                RequestPayer="requester",
            )
        except ClientError as e:
            if debugging:
                logging.error(e)
            return

    template = response["Body"].read()

    try:
        template_json = json.loads(template)
    except ValueError as e:
        logging.error(e)
        return

    resp["study"] = {
        "uuid": template_json.get("uuid"),
        "name": template_json.get("name"),
        "description": template_json.get("description"),
    }


# Constructs a table with where keys are the normalized (lowercased) file types
# and the values an array of possible viewers
def build_filetypes_table(osparc_viewers):
    table = {}
    for viewer in osparc_viewers:
        filetype = viewer["file_type"].lower()
        del viewer["file_type"]
        if not table.get(filetype, False):
            table[filetype] = []
        table[filetype].append(viewer)
    return table

@app.route("/sim/dataset/<id_>")
def sim_dataset(id_):
    if request.method == "GET":
        try:
            req = requests.get("{}/datasets/{}".format(Config.DISCOVER_API_HOST, id_))
            if req.ok:
                json_data = req.json()
                inject_markdown(json_data)
                inject_template_data(json_data)
                return jsonify(json_data)
        except Exception as ex:
            logging.error(f"Could not fetch SIM dataset {id_}", ex)
        return abort(404, description="Resource not found")

@app.route("/sim/dataset/<id_>/versions/<version_>")
def sim_dataset_versions(id_, version_):
    if request.method == "GET":
        try:
            req = requests.get("{}/datasets/{}/versions/{}".format(Config.DISCOVER_API_HOST, id_, version_))
            if req.ok:
                json_data = req.json()
                inject_markdown(json_data)
                inject_template_data(json_data)
                return jsonify(json_data)
        except Exception as ex:
            logging.error(f"Could not fetch SIM dataset {id_} version {version_}", ex)
        return abort(404, description="Resource not found")



@app.route("/get_osparc_data")
def get_osparc_data():
    return jsonify(osparc_data)


@app.route('/sim/service')
def osparc_search():
    if request.method == 'GET':
        search = request.args.get('search')
        limit = request.args.get('limit', default=5, type=int)
        skip = request.args.get('skip', default=0, type=int)
        results = osparc_services.search_services(search, limit, skip)
        return jsonify(results)


@app.route('/sim/file')
def osparc_extensions():
    if request.method == 'GET':
        extensions = osparc_services.file_extensions
        return jsonify({
            "file_viewers": extensions
        })


@app.route("/project/<project_id>", methods=["GET"])
def datasets_by_project_id(project_id):
    datasets = get_associated_datasets(project_id)

    if len(datasets['hits']) > 0:
        return jsonify(datasets['hits'])
    else:
        abort(404, description="Resource not found")


@app.route("/get_featured_datasets_identifiers", methods=["GET"])
def get_featured_datasets_identifiers():
    return {'identifiers': get_featured_datasets()}

@app.route("/get_featured_dataset", methods=["GET"])
@cache.cached(timeout=300)
def get_featured_dataset():
    featured_dataset_id = get_featured_dataset_id_table_state(featuredDatasetIdSelectorTable)["featured_dataset_id"]
    if featured_dataset_id == -1:
        # In case there was an error while setting the id, just return a default dataset so the homepage does not break.
        featured_dataset_id = 32
    try:
        response = requests.get("{}/datasets?ids={}".format(Config.DISCOVER_API_HOST, featured_dataset_id)).json()
        # in case the dataset has been unpublished, just return default
        if response['datasets'] == []:
            response = requests.get("{}/datasets?ids={}".format(Config.DISCOVER_API_HOST, 32)).json()
        return response
    except Exception as ex:
        logging.error(f"Could not get featured dataset {featured_dataset_id}", ex)
    abort(404, description="An error occured while fetching the resource")


@app.route("/get_owner_email/<int:owner_id>", methods=["GET"])
def get_owner_email(owner_id):
    # Filter to find user based on provided int id
    org = ps._api._organization
    members = ps._api.organizations.get_members(org)
    res = [x for x in members if x.int_id == owner_id]

    if not res:
        abort(404, description="Owner not found")
    else:
        return jsonify({"email": res[0].email})

# Get information of the latest body scaffold for species.
# This endpoint returns the metadata file path, bucket,
# dataset id and version which can be used to construct the url
@app.route("/get_body_scaffold_info/<species>", methods=["GET"])
def get_body_scaffold_info(species):
    id = get_body_scaffold_dataset_id(species)
    if id:
        query = create_pennsieve_identifier_query(id)
        result = process_get_first_scaffold_info(dataset_search(query))
        if result:
            return result

    return abort(404, description=f"Whole body info not found for {species}")

@app.route("/thumbnail/<image_id>", methods=["GET"])
def thumbnail_by_image_id(image_id, recursive_call=False):
    bl = Biolucida()

    try:
        with biolucida_lock:
            if not bl.token():
                authenticate_biolucida()

        url = Config.BIOLUCIDA_ENDPOINT + "/thumbnail/{0}".format(image_id)
        headers = {
            'token': bl.token(),
        }

        response = requests.request("GET", url, headers=headers)
        encoded_content = base64.b64encode(response.content)
        # Response from this endpoint is binary on success so the easiest thing to do is
        # check for an error response in encoded form.
        if encoded_content == b'eyJzdGF0dXMiOiJBZG1pbiB1c2VyIGF1dGhlbnRpY2F0aW9uIHJlcXVpcmVkIHRvIHZpZXcvZWRpdCB1c2VyIGluZm8uIFlvdSBtYXkgbmVlZCB0byBsb2cgb3V0IGFuZCBsb2cgYmFjayBpbiB0byByZXZlcmlmeSB5b3VyIGNyZWRlbnRpYWxzLiJ9' \
                and not recursive_call:
            # Authentication failure, try again after resetting token.
            with biolucida_lock:
                bl.set_token('')

            encoded_content = thumbnail_by_image_id(image_id, True)

        return encoded_content
    except Exception as ex:
        logging.error(f"Could not get the thumbnail for {image_id}", ex)
    return abort(404, "An error occured while fetching the thumbnail")


@app.route("/image/<image_id>", methods=["GET"])
def image_info_by_image_id(image_id):
    url = Config.BIOLUCIDA_ENDPOINT + "/image/info/{0}".format(image_id)
    try:
        response = requests.request("GET", url)
        return process_biolucida_result(response.json())
    except Exception as ex:
        logging.error(f"Could not get image info for {image_id}", ex)
    return abort(404, "An error occured while getting the image's info")


@app.route("/image_search/<dataset_id>", methods=["GET"])
def image_search_by_dataset_id(dataset_id):
    url = Config.BIOLUCIDA_ENDPOINT + "/imagemap/search_dataset/discover/{0}".format(dataset_id)
    try:
        response = requests.request("GET", url)
        return response.json()
    except Exception as ex:
        logging.error(f"Could not search images for dataset {dataset_id}", ex)
    return {"error": "An error occured while searching images for dataset"}, 404


@app.route("/image_xmp_info/<image_id>", methods=["GET"])
def image_xmp_info(image_id):
    url = Config.BIOLUCIDA_ENDPOINT + "/image/xmpmetadata/{0}".format(image_id)
    try:
        result = requests.request("GET", url)
    except requests.exceptions.ConnectionError:
        return abort(400, description="Unable to make a connection to Biolucida.")

    response = result.json()
    if response['status'] == 'success':
        return process_biolucida_results(response['data'])

    return abort(400, description=f"XMP info not found for {image_id}")


@app.route("/image_blv_link/<image_id>", methods=["GET"])
def image_blv_link(image_id):
    url = Config.BIOLUCIDA_ENDPOINT + "/image/blv_link/{0}".format(image_id)
    try:
        result = requests.request("GET", url)
    except requests.exceptions.ConnectionError:
        return abort(400, description="Unable to make a connection to Biolucida.")

    response = result.json()
    if response['status'] == 'success':
        return jsonify({'link': response['link']})

    return abort(400, description=f"BLV link not found for {image_id}")


def authenticate_biolucida():
    bl = Biolucida()
    url = Config.BIOLUCIDA_ENDPOINT + "/authenticate"

    payload = {'username': Config.BIOLUCIDA_USERNAME,
               'password': Config.BIOLUCIDA_PASSWORD,
               'token': ''}
    files = [
    ]
    headers = {}

    response = requests.request("POST", url, headers=headers, data=payload, files=files)
    if response.status_code == requests.codes.ok:
        content = response.json()
        bl.set_token(content['token'])


def get_share_link(table):
    # Do not commit to database when testing
    commit = True
    if app.config["TESTING"]:
        commit = False
    if table:
        json_data = request.get_json()
        if json_data and 'state' in json_data:
            state = json_data['state']
            uuid = table.pushState(state, commit)
            return jsonify({"uuid": uuid})
        abort(400, description="State not specified")
    else:
        abort(404, description="Database not available")


def get_saved_state(table):
    if table:
        json_data = request.get_json()
        if json_data and 'uuid' in json_data:
            uuid = json_data['uuid']
            state = table.pullState(uuid)
            if state:
                return jsonify({"state": table.pullState(uuid)})
        abort(400, description="Key missing or did not find a match")
    else:
        abort(404, description="Database not available")


# Get the share link for the current map content.
@app.route("/map/getshareid", methods=["POST"])
def get_map_share_link():
    return get_share_link(maptable)


# Get the map state using the share link id.
@app.route("/map/getstate", methods=["POST"])
def get_map_state():
    return get_saved_state(maptable)


# Get the share link for the current map content.
@app.route("/scaffold/getshareid", methods=["POST"])
def get_scaffold_share_link():
    return get_share_link(scaffoldtable)


# Get the map state using the share link id.
@app.route("/scaffold/getstate", methods=["POST"])
def get_scaffold_state():
    return get_saved_state(scaffoldtable)


@app.route("/tasks", methods=["POST"])
def create_wrike_task():
    form = request.form
    if "captcha_token" in form:
        try:
            captchaReq = requests.post(
                url=Config.TURNSTILE_URL,
                json={
                    "secret": Config.NUXT_TURNSTILE_SECRET_KEY,
                    "response": form["captcha_token"]
                }
            )
            captchaResp = captchaReq.json()
            if "success" not in captchaResp or not captchaResp["success"]:
                return { "error": "Failed Captcha Validation" }, 409
        except Exception as ex:
            logging.error("Could not validate captcha, bypassing validation", ex)
    elif not app.config['TESTING']:
        return { "error": "Failed Captcha Validation" }, 409
    # captcha all good
    if form and 'title' in form and 'description' in form:
        title = form["title"]
        description = form["description"]
        newTaskDescription = form["description"]

        hed = { 'Authorization': 'Bearer ' + Config.WRIKE_TOKEN }
        ## Updated Wrike Space info based off type of task. We default to drc_feedback folder if type is not present.
        url = 'https://www.wrike.com/api/v4/folders/' + Config.DRC_FEEDBACK_FOLDER_ID + '/tasks'
        followers = [Config.CCB_HEAD_WRIKE_ID, Config.DAT_CORE_TECH_LEAD_WRIKE_ID, Config.MAP_CORE_TECH_LEAD_WRIKE_ID, Config.K_CORE_TECH_LEAD_WRIKE_ID, Config.SIM_CORE_TECH_LEAD_WRIKE_ID, Config.MODERATOR_WRIKE_ID]
        responsibles = [Config.CCB_HEAD_WRIKE_ID, Config.DAT_CORE_TECH_LEAD_WRIKE_ID, Config.MAP_CORE_TECH_LEAD_WRIKE_ID, Config.K_CORE_TECH_LEAD_WRIKE_ID, Config.SIM_CORE_TECH_LEAD_WRIKE_ID, Config.MODERATOR_WRIKE_ID]
        customStatus = Config.DRC_WRIKE_CUSTOM_STATUS_ID
        taskType = ""
        templateTaskId = ""
        templateSubTaskIds = []
        if form and 'type' in form:
            taskType = form["type"]
        if (taskType == "news"):
          url = 'https://www.wrike.com/api/v4/folders/' + Config.NEWS_AND_EVENTS_FOLDER_ID + '/tasks'
          followers = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          responsibles = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          customStatus = Config.COMMS_WRIKE_CUSTOM_STATUS_ID
          templateTaskId = Config.NEWS_TEMPLATE_TASK_ID
        if (taskType == "event"):
          url = 'https://www.wrike.com/api/v4/folders/' + Config.NEWS_AND_EVENTS_FOLDER_ID + '/tasks'
          followers = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          responsibles = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          customStatus = Config.COMMS_WRIKE_CUSTOM_STATUS_ID
          templateTaskId = Config.EVENT_TEMPLATE_TASK_ID
        elif (taskType == "toolsAndResources"):
          url = 'https://www.wrike.com/api/v4/folders/' + Config.TOOLS_AND_RESOURCES_FOLDER_ID + '/tasks'
          followers = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          responsibles = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          customStatus = Config.COMMS_WRIKE_CUSTOM_STATUS_ID
          templateTaskId = Config.TOOLS_AND_RESOURCES_TEMPLATE_TASK_ID
        elif (taskType == "communitySpotlight"):
          url = 'https://www.wrike.com/api/v4/folders/' + Config.COMMUNITY_SPOTLIGHT_FOLDER_ID + '/tasks'
          followers = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          responsibles = [Config.COMMS_LEAD_1_WRIKE_ID, Config.COMMS_LEAD_2_WRIKE_ID, Config.COMMS_LEAD_3_WRIKE_ID]
          customStatus = Config.COMMS_WRIKE_CUSTOM_STATUS_ID
          templateTaskId = Config.COMMUNITY_SPOTLIGHT_TEMPLATE_TASK_ID
        elif (taskType == "research"):
          followers.extend([Config.SUE_WRIKE_ID, Config.JYL_WRIKE_ID])
          responsibles.extend([Config.SUE_WRIKE_ID, Config.JYL_WRIKE_ID])

        if (templateTaskId != ""):
          templateUrl = 'https://www.wrike.com/api/v4/tasks/' + templateTaskId
          templateResp = requests.get(
            url=templateUrl,
            headers=hed
          )
          if 'data' in templateResp.json() and templateResp.json()["data"] != []:
            newTaskDescription = templateResp.json()["data"][0]["description"] + description
            templateSubTaskIds = templateResp.json()["data"][0]["subTaskIds"]

        data = {
            "title": title,
            "description": newTaskDescription,
            "customStatus": customStatus,
            "followers": followers,
            "responsibles": responsibles,
            "follow": False,
            "dates": {"type": "Backlog"}
        }

        resp = requests.post(
            url=url,
            json=data,
            headers=hed
        )

        # add the file as an attachment to the newly created ticket
        files = request.files
        if 'data' in resp.json() and resp.json()["data"] != []:
          new_task_id = resp.json()["data"][0]["id"]
          if files and 'attachment' in files:
              attachment = files['attachment']
              file_data = attachment.read()
              file_name = attachment.filename
              content_type = attachment.content_type
              headers = {
                  'Authorization': 'Bearer ' +  Config.WRIKE_TOKEN,
                  'X-File-Name': file_name,
                  'content-type': content_type,
                  'X-Requested-With': 'XMLHttpRequest'
                }
              attachment_url = "https://www.wrike.com/api/v4/tasks/" + new_task_id + "/attachments"

              try:
                requests.post(
                  url=attachment_url,
                  data=file_data,
                  headers=headers
                )
              except Exception as e:
                print(e)

          # create copies of all the templates subtasks and add them to the newly created ticket
          for subTaskId in templateSubTaskIds:
            subTaskTemplateUrl = 'https://www.wrike.com/api/v4/tasks/' + subTaskId
            subTaskTemplateResp = requests.get(
              url = subTaskTemplateUrl,
              headers=hed
            )
            if 'data' in subTaskTemplateResp.json() and subTaskTemplateResp.json()["data"] != []:
              subTaskData = {
                "title": subTaskTemplateResp.json()["data"][0]["title"],
                "description": subTaskTemplateResp.json()["data"][0]["description"],
                "customStatus": subTaskTemplateResp.json()["data"][0]["customStatusId"],
                "followers": subTaskTemplateResp.json()["data"][0]["followerIds"],
                "responsibles": subTaskTemplateResp.json()["data"][0]["responsibleIds"],
                "follow": False,
                "superTasks": [new_task_id],
                "dates": {"type": "Backlog"}
              }
              requests.post(
                url=url,
                json=subTaskData,
                headers=hed
              )

        if (resp.status_code == 200):
          if 'userEmail' in form and form['userEmail'] and 'sendCopy' in form and form['sendCopy'] == 'true':
            # default to bug form if task type not specified
            subject = 'SPARC Reported Error/Issue Submission'
            body = issue_reporting_email.substitute({ 'message': description })
            if (taskType == "feedback"):
              subject = 'SPARC Feedback Submission'
              body = feedback_email.substitute({ 'message': description })
            elif (taskType == "interest"):
              subject = 'SPARC Service Interest Submission'
              body = service_interest_email.substitute({ 'message': description })
            elif (taskType == "general"):
              subject = 'SPARC Question or Inquiry Submission'
              body = general_interest_email.substitute({ 'message': description })
            elif (taskType == "research"):
              subject = 'SPARC Research Submission'
              body = creation_request_confirmation_email.substitute({ 'message': description })
            elif (taskType == "news"):
              subject = 'SPARC News Submission'
              body = creation_request_confirmation_email.substitute({ 'message': description })
            elif (taskType == "event"):
              subject = 'SPARC Event Submission'
              body = creation_request_confirmation_email.substitute({ 'message': description })
            elif (taskType == "toolsAndResources"):
              subject = 'SPARC Tool/Resource Submission'
              body = creation_request_confirmation_email.substitute({ 'message': description })
            elif (taskType == "communitySpotlight"):
              subject = 'SPARC Story Submission'
              body = creation_request_confirmation_email.substitute({ 'message': description })
            userEmail = form['userEmail']
            if len(userEmail) > 0:
              email_sender.sendgrid_email(Config.SES_SENDER, form['userEmail'], subject, body)

          return jsonify(
            title=title,
            description=description,
            task_id=resp.json()["data"][0]["id"]
          )
        else:
            return resp.json()
    else:
        abort(400, description="Missing title or description")


@app.route("/mailchimp_subscribe", methods=["POST"])
def subscribe_to_mailchimp():
    json_data = request.get_json()
    if json_data and 'email_address' in json_data and 'first_name' in json_data and 'last_name' in json_data:
        email_address = json_data["email_address"]
        first_name = json_data['first_name']
        last_name = json_data['last_name']
        auth = HTTPBasicAuth('AnyUser', Config.MAILCHIMP_API_KEY)
        url = 'https://us2.api.mailchimp.com/3.0/lists/c81a347bd8/members/' + email_address

        data = {
            "email_address": email_address,
            "status": "subscribed",
            "merge_fields": {
                "FNAME": first_name,
                "LNAME": last_name
            }
        }
        try:
            resp = requests.put(
                url=url,
                json=data,
                auth=auth
            )

            if resp.status_code == 200:
                return resp.json()
            else:
                return "Failed to subscribe user with response: " + resp.json()
        except Exception as ex:
            logging.error("Could not subscribe to newsletter", ex)
        return {"error": "An error occured while trying to subscribe to the newsletter"}, 500
    else:
        abort(400, description="Missing email_address, first_name or last_name")


@app.route("/mailchimp_unsubscribe", methods=["POST"])
def unsubscribe_to_mailchimp():
    json_data = request.get_json()
    if json_data and "email_address" in json_data:
        email_address = json_data["email_address"]
        auth = HTTPBasicAuth('AnyUser', Config.MAILCHIMP_API_KEY)
        url = "https://us2.api.mailchimp.com/3.0/lists/c81a347bd8/members/" + email_address

        data = {
            "status": "unsubscribed",
        }
        try:
            resp = requests.put(
                url=url,
                json=data,
                auth=auth
            )

            if resp.status_code == 200:
                return resp.json()
            else:
                return "Failed to unsubscribe user with response: " + resp.json()
        except Exception as ex:
            logging.error("Could not unsubscribe to newsletter", ex)
        return {"error": "An error occured while trying to unsubscribe to the newsletter"}, 500
    else:
        abort(400, description="Missing email_address")

@app.route("/mailchimp_member_info/<email_address>", methods=["GET"])
def get_mailchimp_member_info(email_address):
    if email_address:
        auth = HTTPBasicAuth('AnyUser', Config.MAILCHIMP_API_KEY)
        url = 'https://us2.api.mailchimp.com/3.0/lists/c81a347bd8/members/' + email_address

        try:
            resp = requests.get(
                url=url,
                auth=auth
            )

            if resp.status_code == 200:
                return resp.json()
            else:
                return "Failed to get member info with response: " + resp.json()
        except Exception as ex:
            logging.error(f"Failed to get member info for {email_address}", ex)
        return {"error": "Could not get member info from MailChimp"}, 500
    else:
        abort(400, description="Missing email_address")


# Get list of available name / curie pair
@app.route("/get-organ-curies/")
def get_available_uberonids():
    species = request.args.getlist('species')

    requestBody = create_request_body_for_curies(species)

    result = {}

    try:
        response = requests.post(
            f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
            json=requestBody)
        result = reform_curies_results(response.json())
    except BaseException as ex:
        logging.error("Failed getting Uberon IDs", ex)
        return {
            "message": "Could not parse SciCrunch output, please try again later",
            "error": "BaseException"
        }, 502

    return jsonify(result)


# Get list of terms a level up/down from
@app.route("/get-related-terms/<query>")
def get_related_terms(query):

    payload = {
        'direction': request.args.get('direction', default='OUTGOING'),
        'relationshipType': request.args.get('relationshipType', default='BFO:0000050'),
        'entail':  request.args.get('entail', default='true'),
        'api_key': Config.KNOWLEDGEBASE_KEY
    }

    result = {}

    try:
        response = requests.get(
            f'{Config.SCI_CRUNCH_SCIGRAPH_HOST}/graph/neighbors/{query}',
            params=payload)
        result = reform_related_terms(response.json())
    except BaseException as ex:
        logging.error(f"Failed getting related terms with payload {payload}", ex)
        return {
            "message": "Could not parse SciCrunch output, please try again later",
            "error": "BaseException"
        }, 502

    return jsonify(result)

@app.route("/simulation_ui_file/<identifier>")
def simulation_ui_file(identifier):

    results = process_results(dataset_search(create_pennsieve_identifier_query(identifier)))
    results_json = json.loads(results.data)

    try:
        item = results_json["results"][0]
        uri = item["s3uri"]
        path = item["abi-simulation-file"][0]["dataset"]["path"]
        key = re.sub(r"s3://[^/]*/", "", f"{uri}files/{path}")
        s3_bucket_name = re.sub(r"s3://|/.*", "", uri)

        return jsonify(json.loads(direct_download_url(key, s3_bucket_name)))
    except Exception:
        abort(404, description="no simulation UI file could be found")


@app.route("/pmr_file", methods=["POST"])
def pmr_file():
    data = request.get_json()
    if data and "path" in data:
        try:
            resp = requests.post(f"{Config.PMR_HOST}/{data['path']}")
            if resp.status_code == 200:
                return base64.b64encode(resp.content)
            else:
                return resp.json()
        except:
            abort(400, description="invalid path")
    else:
        abort(400, description="missing path")


@app.route("/start_simulation", methods=["POST"])
def start_simulation():
    data = request.get_json()

    if data and "solver" in data and "name" in data["solver"] and "version" in data["solver"]:
        return json.dumps(do_start_simulation(data))
    else:
        abort(400, description="Missing solver name and/or solver version")


@app.route("/check_simulation", methods=["POST"])
def check_simulation():
    data = request.get_json()

    if data and "job_id" in data and "solver" in data and "name" in data["solver"] and "version" in data["solver"]:
        return json.dumps(do_check_simulation(data))
    else:
        abort(400, description="Missing solver name, solver version and/or job id")


@app.route("/pmr_latest_exposure", methods=["POST"])
def pmr_latest_exposure():
    data = request.get_json()

    if data and "workspace_url" in data:
        try:
            resp = requests.get(data["workspace_url"],
                                headers={"Accept": "application/vnd.physiome.pmr2.json.1"})
            if resp.status_code == 200:
                try:
                    # Return the latest exposure for the given workspace.
                    url = resp.json()["collection"]["items"][0]["links"][0]["href"]
                except:
                    # There is no latest exposure for the given workspace.
                    url = ""
                return jsonify(
                    url=url
                )
            else:
                return resp.json()
        except:
            abort(400, description="Invalid workspace URL")
    else:
        abort(400, description="Missing workspace URL")


@app.route("/onto_term_lookup")
def find_by_onto_term():
    term = request.args.get('term')

    headers = {
        'Accept': 'application/json',
    }

    params = {
        "api_key": Config.KNOWLEDGEBASE_KEY
    }

    query = create_onto_term_query(term)

    try:
        response = requests.get(f'{Config.SCI_CRUNCH_INTERLEX_HOST}/_search', headers=headers, params=params, json=query)

        results = response.json()
        hits = results['hits']['hits']
        total = results['hits']['total']
        if total == 1:
            result = hits[0]
            json_data = result['_source']
        else:
            json_data = {'label': 'not found'}

        return json_data
    except Exception as ex:
        logging.error("An error occured while fetching from SciCrunch", ex)
    return abort(500)


@app.route("/search-readme/<query>", methods=["GET"])
def search_readme(query):
    url = 'https://dash.readme.com/api/v1/docs/search?search=' + query
    headers = { 'Authorization': 'Basic ' + Config.README_API_KEY }

    try:
        response = requests.post(
          url = url,
          headers = headers
        )
        return response.json()
    except requests.exceptions.HTTPError as err:
        logging.error(err)
        return {
            "error": str(err),
            "message": "Readme is not currently reachable, please try again later"
        }, 502

@app.route("/metrics", methods=["GET"])
def metrics():
    return usage_metrics

# Callback endpoint for contentful event updated webhook that gets triggered when an event is updated in Contentful
@app.route("/event_updated", methods=["POST"])
def event_updated():
    # the webhook secret key is configured with the same value as the cda access token. If the cda access token is updated then we must update this as well.
    secret_key = request.headers.get('event_updated_secret_key')
    if secret_key != Config.CTF_CDA_ACCESS_TOKEN:
        abort(403, description=f'Invalid secret key: {secret_key}')
    else:
        event = request.get_json()
        if event:
            try:
                return update_event_sort_order(event)
            except:
                abort(400, description=f'Invalid event data: {event}')
        else:
            abort(400, description="Missing event data")

@app.route("/all_dataset_ids", methods=["GET"])
def all_dataset_ids():
    list = get_all_dataset_ids()
    string_list = [str(element) for element in list]
    delimiter = ", "
    return delimiter.join(string_list)