"""Main routing table for GN2"""

import traceback  # for error page
import os        # for error gifs
import random    # for random error gif
import datetime  # for errors
import sys
import csv
import json
import xlsxwriter
import io  # Todo: Use cStringIO?
import MySQLdb

from zipfile import ZipFile, ZIP_DEFLATED

import numpy as np
import pickle as pickle
import uuid

import flask
import base64
import array
import sqlalchemy
from wqflask import app

from gn3.db import diff_from_dict
from gn3.db import fetchone
from gn3.db import insert
from gn3.db import update
from gn3.db.metadata_audit import MetadataAudit
from gn3.db.phenotypes import Phenotype
from gn3.db.phenotypes import Publication
from gn3.db.phenotypes import PublishXRef


from flask import current_app
from flask import g
from flask import Response
from flask import request
from flask import make_response
from flask import render_template
from flask import send_from_directory
from flask import redirect
from flask import url_for
from flask import send_file

# Some of these (like collect) might contain endpoints, so they're still used.
# Blueprints should probably be used instead.
from wqflask import collect
from wqflask import search_results
from wqflask import server_side
from base.data_set import create_dataset  # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
from wqflask.show_trait import export_trait_data
from wqflask.heatmap import heatmap
from wqflask.external_tools import send_to_bnw
from wqflask.external_tools import send_to_webgestalt
from wqflask.external_tools import send_to_geneweaver
from wqflask.comparison_bar_chart import comparison_bar_chart
from wqflask.marker_regression import run_mapping
from wqflask.marker_regression import display_mapping_results
from wqflask.network_graph import network_graph
from wqflask.correlation import show_corr_results
from wqflask.correlation.correlation_gn3_api import compute_correlation
from wqflask.correlation_matrix import show_corr_matrix
from wqflask.correlation import corr_scatter_plot
from wqflask.wgcna import wgcna_analysis
from wqflask.ctl import ctl_analysis
from wqflask.snp_browser import snp_browser
from wqflask.search_results import SearchResultPage
from wqflask.export_traits import export_search_results_csv
from wqflask.gsearch import GSearch
from wqflask.update_search_results import GSearch as UpdateGSearch
from wqflask.docs import Docs, update_text
from wqflask.decorators import admin_login_required
from wqflask.db_info import InfoPage

from utility import temp_data
from utility.tools import SQL_URI
from utility.tools import TEMPDIR
from utility.tools import USE_REDIS
from utility.tools import GN_SERVER_URL
from utility.tools import GN_VERSION
from utility.tools import JS_TWITTER_POST_FETCHER_PATH
from utility.tools import JS_GUIX_PATH
from utility.helper_functions import get_species_groups
from utility.authentication_tools import check_resource_availability
from utility.redis_tools import get_redis_conn


from base.webqtlConfig import GENERATED_IMAGE_DIR, DEFAULT_PRIVILEGES
from utility.benchmark import Bench

from pprint import pformat as pf

from wqflask.database import db_session


import utility.logger

Redis = get_redis_conn()

logger = utility.logger.getLogger(__name__)


@app.before_request
def connect_db():
    logger.info("@app.before_request connect_db")
    db = getattr(g, '_database', None)
    if db is None:
        g.db = g._database = sqlalchemy.create_engine(
            SQL_URI, encoding="latin1")
        logger.debug(g.db)


@app.before_request
def check_access_permissions():
    logger.debug("@app.before_request check_access_permissions")
    if 'dataset' in request.args:
        permissions = DEFAULT_PRIVILEGES
        if request.args['dataset'] != "Temp":
            dataset = create_dataset(request.args['dataset'])

            if dataset.type == "Temp":
                permissions = DEFAULT_PRIVILEGES
            elif 'trait_id' in request.args:
                permissions = check_resource_availability(
                    dataset, request.args['trait_id'])
            elif dataset.type != "Publish":
                permissions = check_resource_availability(dataset)

        if type(permissions['data']) is list:
            if 'view' not in permissions['data']:
                return redirect(url_for("no_access_page"))
        else:
            if permissions['data'] == 'no-access':
                return redirect(url_for("no_access_page"))


@app.teardown_appcontext
def shutdown_session(exception=None):
    db = getattr(g, '_database', None)
    if db is not None:
        logger.debug("remove db_session")
        db_session.remove()
        g.db = None


@app.errorhandler(Exception)
def handle_bad_request(e):
    err_msg = str(e)
    logger.error(err_msg)
    logger.error(request.url)
    # get the stack trace and send it to the logger
    exc_type, exc_value, exc_traceback = sys.exc_info()
    logger.error(traceback.format_exc())
    now = datetime.datetime.utcnow()
    time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
    formatted_lines = [request.url
                       + " (" + time_str + ")"] + traceback.format_exc().splitlines()

    # Handle random animations
    # Use a cookie to have one animation on refresh
    animation = request.cookies.get(err_msg[:32])
    if not animation:
        list = [fn for fn in os.listdir(
            "./wqflask/static/gif/error") if fn.endswith(".gif")]
        animation = random.choice(list)

    resp = make_response(render_template("error.html", message=err_msg,
                                         stack=formatted_lines, error_image=animation, version=GN_VERSION))

    # logger.error("Set cookie %s with %s" % (err_msg, animation))
    resp.set_cookie(err_msg[:32], animation)
    return resp


@app.route("/authentication_needed")
def no_access_page():
    return render_template("new_security/not_authenticated.html")


@app.route("/")
def index_page():
    logger.info("Sending index_page")
    logger.info(request.url)
    params = request.args
    if 'import_collections' in params:
        import_collections = params['import_collections']
        if import_collections == "true":
            g.user_session.import_traits_to_user(params['anon_id'])
    return render_template("index_page.html", version=GN_VERSION)


@app.route("/tmp/<img_path>")
def tmp_page(img_path):
    logger.info("In tmp_page")
    logger.info("img_path:", img_path)
    logger.info(request.url)
    initial_start_vars = request.form
    logger.info("initial_start_vars:", initial_start_vars)
    imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
    imgdata = imgfile.read()
    imgB64 = base64.b64encode(imgdata)
    bytesarray = array.array('B', imgB64)
    return render_template("show_image.html",
                           img_base64=bytesarray)


@app.route("/js/<path:filename>")
def js(filename):
    js_path = JS_GUIX_PATH
    name = filename
    if 'js_alt/' in filename:
        js_path = js_path.replace('genenetwork2/javascript', 'javascript')
        name = name.replace('js_alt/', '')
    return send_from_directory(js_path, name)


@app.route("/css/<path:filename>")
def css(filename):
    js_path = JS_GUIX_PATH
    name = filename
    if 'js_alt/' in filename:
        js_path = js_path.replace('genenetwork2/javascript', 'javascript')
        name = name.replace('js_alt/', '')
    return send_from_directory(js_path, name)


@app.route("/twitter/<path:filename>")
def twitter(filename):
    return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename)


@app.route("/search", methods=('GET',))
def search_page():
    logger.info("in search_page")
    logger.info(request.url)
    result = None
    if USE_REDIS:
        with Bench("Trying Redis cache"):
            key = "search_results:v1:" + \
                json.dumps(request.args, sort_keys=True)
            logger.debug("key is:", pf(key))
            result = Redis.get(key)
            if result:
                logger.info("Redis cache hit on search results!")
                result = pickle.loads(result)
    else:
        logger.info("Skipping Redis cache (USE_REDIS=False)")

    logger.info("request.args is", request.args)
    the_search = SearchResultPage(request.args)
    result = the_search.__dict__
    valid_search = result['search_term_exists']

    if USE_REDIS and valid_search:
        Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
        Redis.expire(key, 60 * 60)

    if valid_search:
        return render_template("search_result_page.html", **result)
    else:
        return render_template("search_error.html")


@app.route("/search_table", methods=('GET',))
def search_page_table():
    logger.info("in search_page table")
    logger.info(request.url)

    logger.info("request.args is", request.args)
    the_search = search_results.SearchResultPage(request.args)

    logger.info(type(the_search.trait_list))
    logger.info(the_search.trait_list)

    current_page = server_side.ServerSideTable(
        len(the_search.trait_list),
        the_search.trait_list,
        the_search.header_data_names,
        request.args,
    ).get_page()

    return flask.jsonify(current_page)


@app.route("/gsearch", methods=('GET',))
def gsearchact():
    logger.info(request.url)
    result = GSearch(request.args).__dict__
    type = request.args['type']
    if type == "gene":
        return render_template("gsearch_gene.html", **result)
    elif type == "phenotype":
        return render_template("gsearch_pheno.html", **result)

@app.route("/gsearch_table", methods=('GET',))
def gsearchtable():
    logger.info(request.url)

    gsearch_table_data = GSearch(request.args)
    current_page = server_side.ServerSideTable(
        gsearch_table_data.trait_count,
        gsearch_table_data.trait_list,
        gsearch_table_data.header_data_names,
        request.args,
    ).get_page()

    return flask.jsonify(current_page)

@app.route("/gsearch_updating", methods=('POST',))
def gsearch_updating():
    logger.info("REQUEST ARGS:", request.values)
    logger.info(request.url)
    result = UpdateGSearch(request.args).__dict__
    return result['results']


@app.route("/docedit")
def docedit():
    logger.info(request.url)
    try:
        if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
            doc = Docs(request.args['entry'], request.args)
            return render_template("docedit.html", **doc.__dict__)
        else:
            return "You shouldn't be here!"
    except:
        return "You shouldn't be here!"


@app.route('/generated/<filename>')
def generated_file(filename):
    logger.info(request.url)
    return send_from_directory(GENERATED_IMAGE_DIR, filename)


@app.route("/help")
def help():
    logger.info(request.url)
    doc = Docs("help", request.args)
    return render_template("docs.html", **doc.__dict__)


@app.route("/wgcna_setup", methods=('POST',))
def wcgna_setup():
    # We are going to get additional user input for the analysis
    logger.info("In wgcna, request.form is:", request.form)
    logger.info(request.url)
    # Display them using the template
    return render_template("wgcna_setup.html", **request.form)


@app.route("/wgcna_results", methods=('POST',))
def wcgna_results():
    logger.info("In wgcna, request.form is:", request.form)
    logger.info(request.url)
    # Start R, load the package and pointers and create the analysis
    wgcna = wgcna_analysis.WGCNA()
    # Start the analysis, a wgcnaA object should be a separate long running thread
    wgcnaA = wgcna.run_analysis(request.form)
    # After the analysis is finished store the result
    result = wgcna.process_results(wgcnaA)
    # Display them using the template
    return render_template("wgcna_results.html", **result)


@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
    # We are going to get additional user input for the analysis
    logger.info("In ctl, request.form is:", request.form)
    logger.info(request.url)
    # Display them using the template
    return render_template("ctl_setup.html", **request.form)


@app.route("/ctl_results", methods=('POST',))
def ctl_results():
    logger.info("In ctl, request.form is:", request.form)
    logger.info(request.url)
    # Start R, load the package and pointers and create the analysis
    ctl = ctl_analysis.CTL()
    # Start the analysis, a ctlA object should be a separate long running thread
    ctlA = ctl.run_analysis(request.form)
    # After the analysis is finished store the result
    result = ctl.process_results(ctlA)
    # Display them using the template
    return render_template("ctl_results.html", **result)


@app.route("/news")
def news():
    doc = Docs("news", request.args)
    return render_template("docs.html", **doc.__dict__)


@app.route("/intro")
def intro():
    doc = Docs("intro", request.args)
    return render_template("docs.html", **doc.__dict__)


@app.route("/tutorials")
def tutorials():
    return render_template("tutorials.html")


@app.route("/credits")
def credits():
    return render_template("credits.html")


@app.route("/update_text", methods=('POST',))
def update_page():
    update_text(request.form)
    doc = Docs(request.form['entry_type'], request.form)
    return render_template("docs.html", **doc.__dict__)


@app.route("/submit_trait")
def submit_trait_form():
    logger.info(request.url)
    species_and_groups = get_species_groups()
    return render_template(
        "submit_trait.html",
        species_and_groups=species_and_groups,
        gn_server_url=GN_SERVER_URL,
        version=GN_VERSION)


@app.route("/trait/<name>/edit/<inbred_set_id>")
@admin_login_required
def edit_trait(name, inbred_set_id):
    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                           user=current_app.config.get("DB_USER"),
                           passwd=current_app.config.get("DB_PASS"),
                           host=current_app.config.get("DB_HOST"))
    publish_xref = fetchone(
        conn=conn,
        table="PublishXRef",
        where=PublishXRef(id_=name,
                          inbred_set_id=inbred_set_id))
    phenotype_ = fetchone(
        conn=conn,
        table="Phenotype",
        where=Phenotype(id_=publish_xref.phenotype_id))
    publication_ = fetchone(
        conn=conn,
        table="Publication",
        where=Publication(id_=publish_xref.publication_id))
    return render_template(
        "edit_trait.html",
        publish_xref=publish_xref,
        phenotype=phenotype_,
        publication=publication_,
        version=GN_VERSION)


@app.route("/trait/update", methods=["POST"])
def update_trait():
    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                           user=current_app.config.get("DB_USER"),
                           passwd=current_app.config.get("DB_PASS"),
                           host=current_app.config.get("DB_HOST"))
    data_ = request.form.to_dict()
    # Run updates:
    phenotype_ = {
        "pre_pub_description": data_.get("pre-pub-desc"),
        "post_pub_description": data_.get("post-pub-desc"),
        "original_description": data_.get("orig-desc"),
        "units": data_.get("units"),
        "pre_pub_abbreviation": data_.get("pre-pub-abbrev"),
        "post_pub_abbreviation": data_.get("post-pub-abbrev"),
        "lab_code": data_.get("labcode"),
        "submitter": data_.get("submitter"),
        "owner": data_.get("owner"),
        "authorized_users": data_.get("authorized-users"),
    }
    updated_phenotypes = update(
        conn, "Phenotype",
        data=Phenotype(**phenotype_),
        where=Phenotype(id_=data_.get("phenotype-id")))
    diff_data = {}
    if updated_phenotypes:
        diff_data.update({"Phenotype": diff_from_dict(old={
            k: data_.get(f"old_{k}") for k, v in phenotype_.items()
            if v is not None}, new=phenotype_)})
    publication_ = {
        "abstract": data_.get("abstract"),
        "authors": data_.get("authors"),
        "title": data_.get("title"),
        "journal": data_.get("journal"),
        "volume": data_.get("volume"),
        "pages": data_.get("pages"),
        "month": data_.get("month"),
        "year": data_.get("year")
    }
    updated_publications = update(
        conn, "Publication",
        data=Publication(**publication_),
        where=Publication(id_=data_.get("pubmed-id",
                                        data_.get("old_id_"))))
    if updated_publications:
        diff_data.update({"Publication": diff_from_dict(old={
            k: data_.get(f"old_{k}") for k, v in publication_.items()
            if v is not None}, new=publication_)})
    author = g.user_session.record.get(b'user_name')
    if diff_data:
        diff_data.update({"dataset_id": data_.get("dataset-name")})
        diff_data.update({"author": author.decode('utf-8')})
        diff_data.update({"timestamp": datetime.datetime.now().strftime(
            "%Y-%m-%d %H:%M:%S")})
        insert(conn,
               table="metadata_audit",
               data=MetadataAudit(dataset_id=data_.get("dataset-name"),
                                  editor=author.decode("utf-8"),
                                  json_data=json.dumps(diff_data)))
    return redirect("/trait/10007/edit/1")


@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
    logger.info(request.url)
    doc = Docs("links")
    return render_template("links.html", **doc.__dict__)


@app.route('/export_trait_excel', methods=('POST',))
def export_trait_excel():
    """Excel file consisting of the sample data from the trait data and analysis page"""
    logger.info("In export_trait_excel")
    logger.info("request.form:", request.form)
    logger.info(request.url)
    trait_name, sample_data = export_trait_data.export_sample_table(
        request.form)

    logger.info("sample_data - type: %s -- size: %s" %
                (type(sample_data), len(sample_data)))

    buff = io.BytesIO()
    workbook = xlsxwriter.Workbook(buff, {'in_memory': True})
    worksheet = workbook.add_worksheet()
    for i, row in enumerate(sample_data):
        for j, column in enumerate(row):
            worksheet.write(i, j, row[j])
    workbook.close()
    excel_data = buff.getvalue()
    buff.close()

    return Response(excel_data,
                    mimetype='application/vnd.ms-excel',
                    headers={"Content-Disposition": "attachment;filename=" + trait_name + ".xlsx"})


@app.route('/export_trait_csv', methods=('POST',))
def export_trait_csv():
    """CSV file consisting of the sample data from the trait data and analysis page"""
    logger.info("In export_trait_csv")
    logger.info("request.form:", request.form)
    logger.info(request.url)
    trait_name, sample_data = export_trait_data.export_sample_table(
        request.form)

    logger.info("sample_data - type: %s -- size: %s" %
                (type(sample_data), len(sample_data)))

    buff = io.StringIO()
    writer = csv.writer(buff)
    for row in sample_data:
        writer.writerow(row)
    csv_data = buff.getvalue()
    buff.close()

    return Response(csv_data,
                    mimetype='text/csv',
                    headers={"Content-Disposition": "attachment;filename=" + trait_name + ".csv"})


@app.route('/export_traits_csv', methods=('POST',))
def export_traits_csv():
    """CSV file consisting of the traits from the search result page"""
    logger.info("In export_traits_csv")
    logger.info("request.form:", request.form)
    logger.info(request.url)
    file_list = export_search_results_csv(request.form)

    if len(file_list) > 1:
        now = datetime.datetime.now()
        time_str = now.strftime('%H:%M_%d%B%Y')
        filename = "export_{}".format(time_str)
        memory_file = io.StringIO()
        with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf:
            for the_file in file_list:
                zf.writestr(the_file[0], the_file[1])

        memory_file.seek(0)

        return send_file(memory_file, attachment_filename=filename + ".zip", as_attachment=True)
    else:
        return Response(file_list[0][1],
                        mimetype='text/csv',
                        headers={"Content-Disposition": "attachment;filename=" + file_list[0][0]})


@app.route('/export_perm_data', methods=('POST',))
def export_perm_data():
    """CSV file consisting of the permutation data for the mapping results"""
    logger.info(request.url)
    perm_info = json.loads(request.form['perm_info'])

    now = datetime.datetime.now()
    time_str = now.strftime('%H:%M_%d%B%Y')

    file_name = "Permutation_" + \
        perm_info['num_perm'] + "_" + perm_info['trait_name'] + "_" + time_str

    the_rows = [
        ["#Permutation Test"],
        ["#File_name: " + file_name],
        ["#Metadata: From GeneNetwork.org"],
        ["#Trait_ID: " + perm_info['trait_name']],
        ["#Trait_description: " + perm_info['trait_description']],
        ["#N_permutations: " + str(perm_info['num_perm'])],
        ["#Cofactors: " + perm_info['cofactors']],
        ["#N_cases: " + str(perm_info['n_samples'])],
        ["#N_genotypes: " + str(perm_info['n_genotypes'])],
        ["#Genotype_file: " + perm_info['genofile']],
        ["#Units_linkage: " + perm_info['units_linkage']],
        ["#Permutation_stratified_by: "
            + ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])],
        ["#RESULTS_1: Suggestive LRS(p=0.63) = "
         + str(np.percentile(np.array(perm_info['perm_data']), 67))],
        ["#RESULTS_2: Significant LRS(p=0.05) = " + str(
            np.percentile(np.array(perm_info['perm_data']), 95))],
        ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(
            np.percentile(np.array(perm_info['perm_data']), 99))],
        ["#Comment: Results sorted from low to high peak linkage"]
    ]

    buff = io.StringIO()
    writer = csv.writer(buff)
    writer.writerows(the_rows)
    for item in perm_info['perm_data']:
        writer.writerow([item])
    csv_data = buff.getvalue()
    buff.close()

    return Response(csv_data,
                    mimetype='text/csv',
                    headers={"Content-Disposition": "attachment;filename=" + file_name + ".csv"})


@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
    logger.info(request.url)
    template_vars = show_trait.ShowTrait(request.form)
    template_vars.js_data = json.dumps(template_vars.js_data,
                                       default=json_default_handler,
                                       indent="   ")
    return render_template("show_trait.html", **template_vars.__dict__)


@app.route("/show_trait")
def show_trait_page():
    logger.info(request.url)
    template_vars = show_trait.ShowTrait(request.args)
    template_vars.js_data = json.dumps(template_vars.js_data,
                                       default=json_default_handler,
                                       indent="   ")
    return render_template("show_trait.html", **template_vars.__dict__)


@app.route("/heatmap", methods=('POST',))
def heatmap_page():
    logger.info("In heatmap, request.form is:", pf(request.form))
    logger.info(request.url)

    start_vars = request.form
    temp_uuid = uuid.uuid4()

    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
    if traits[0] != "":
        version = "v5"
        key = "heatmap:{}:".format(
            version) + json.dumps(start_vars, sort_keys=True)
        logger.info("key is:", pf(key))
        with Bench("Loading cache"):
            result = Redis.get(key)

        if result:
            logger.info("Cache hit!!!")
            with Bench("Loading results"):
                result = pickle.loads(result)

        else:
            logger.info("Cache miss!!!")

            template_vars = heatmap.Heatmap(request.form, temp_uuid)
            template_vars.js_data = json.dumps(template_vars.js_data,
                                               default=json_default_handler,
                                               indent="   ")

            result = template_vars.__dict__

            for item in list(template_vars.__dict__.keys()):
                logger.info(
                    "  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))

            pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
            logger.info("pickled result length:", len(pickled_result))
            Redis.set(key, pickled_result)
            Redis.expire(key, 60 * 60)

        with Bench("Rendering template"):
            rendered_template = render_template("heatmap.html", **result)

    else:
        rendered_template = render_template(
            "empty_collection.html", **{'tool': 'Heatmap'})

    return rendered_template


@app.route("/bnw_page", methods=('POST',))
def bnw_page():
    logger.info("In run BNW, request.form is:", pf(request.form))
    logger.info(request.url)

    start_vars = request.form

    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
    if traits[0] != "":
        template_vars = send_to_bnw.SendToBNW(request.form)

        result = template_vars.__dict__
        rendered_template = render_template("bnw_page.html", **result)
    else:
        rendered_template = render_template(
            "empty_collection.html", **{'tool': 'BNW'})

    return rendered_template


@app.route("/webgestalt_page", methods=('POST',))
def webgestalt_page():
    logger.info("In run WebGestalt, request.form is:", pf(request.form))
    logger.info(request.url)

    start_vars = request.form

    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
    if traits[0] != "":
        template_vars = send_to_webgestalt.SendToWebGestalt(request.form)

        result = template_vars.__dict__
        rendered_template = render_template("webgestalt_page.html", **result)
    else:
        rendered_template = render_template(
            "empty_collection.html", **{'tool': 'WebGestalt'})

    return rendered_template


@app.route("/geneweaver_page", methods=('POST',))
def geneweaver_page():
    logger.info("In run WebGestalt, request.form is:", pf(request.form))
    logger.info(request.url)

    start_vars = request.form

    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
    if traits[0] != "":
        template_vars = send_to_geneweaver.SendToGeneWeaver(request.form)

        result = template_vars.__dict__
        rendered_template = render_template("geneweaver_page.html", **result)
    else:
        rendered_template = render_template(
            "empty_collection.html", **{'tool': 'GeneWeaver'})

    return rendered_template


@app.route("/comparison_bar_chart", methods=('POST',))
def comp_bar_chart_page():
    logger.info("In comp bar chart, request.form is:", pf(request.form))
    logger.info(request.url)

    start_vars = request.form

    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
    if traits[0] != "":
        template_vars = comparison_bar_chart.ComparisonBarChart(request.form)
        template_vars.js_data = json.dumps(template_vars.js_data,
                                           default=json_default_handler,
                                           indent="   ")

        result = template_vars.__dict__
        rendered_template = render_template(
            "comparison_bar_chart.html", **result)
    else:
        rendered_template = render_template(
            "empty_collection.html", **{'tool': 'Comparison Bar Chart'})

    return rendered_template


@app.route("/mapping_results_container")
def mapping_results_container_page():
    return render_template("mapping_results_container.html")


@app.route("/loading", methods=('POST',))
def loading_page():
    # logger.info(request.url)
    initial_start_vars = request.form
    start_vars_container = {}
    n_samples = 0  # ZS: So it can be displayed on loading page
    if 'wanted_inputs' in initial_start_vars:
        wanted = initial_start_vars['wanted_inputs'].split(",")
        start_vars = {}
        for key, value in list(initial_start_vars.items()):
            if key in wanted:
                start_vars[key] = value

        if 'n_samples' in start_vars:
            n_samples = int(start_vars['n_samples'])
        else:
            sample_vals_dict = json.loads(start_vars['sample_vals'])
            if 'group' in start_vars:
                dataset = create_dataset(
                    start_vars['dataset'], group_name=start_vars['group'])
            else:
                dataset = create_dataset(start_vars['dataset'])
            samples = start_vars['primary_samples'].split(",")
            if 'genofile' in start_vars:
                if start_vars['genofile'] != "":
                    genofile_string = start_vars['genofile']
                    dataset.group.genofile = genofile_string.split(":")[0]
                    genofile_samples = run_mapping.get_genofile_samplelist(
                        dataset)
                    if len(genofile_samples) > 1:
                        samples = genofile_samples

            for sample in samples:
                if sample in sample_vals_dict:
                    if sample_vals_dict[sample] != "x":
                        n_samples += 1

        start_vars['n_samples'] = n_samples
        start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']

        start_vars_container['start_vars'] = start_vars
    else:
        start_vars_container['start_vars'] = initial_start_vars

    rendered_template = render_template("loading.html", **start_vars_container)

    return rendered_template


@app.route("/run_mapping", methods=('POST',))
def mapping_results_page():
    initial_start_vars = request.form
    logger.info(request.url)
    temp_uuid = initial_start_vars['temp_uuid']
    wanted = (
        'trait_id',
        'dataset',
        'group',
        'species',
        'samples',
        'vals',
        'sample_vals',
        'first_run',
        'output_files',
        'geno_db_exists',
        'method',
        'mapping_results_path',
        'trimmed_markers',
        'selected_chr',
        'chromosomes',
        'mapping_scale',
        'plotScale',
        'score_type',
        'suggestive',
        'significant',
        'num_perm',
        'permCheck',
        'perm_strata',
        'strat_var',
        'categorical_vars',
        'perm_output',
        'num_bootstrap',
        'bootCheck',
        'bootstrap_results',
        'LRSCheck',
        'covariates',
        'maf',
        'use_loco',
        'manhattan_plot',
        'color_scheme',
        'manhattan_single_color',
        'control_marker',
        'do_control',
        'genofile',
        'genofile_string',
        'pair_scan',
        'startMb',
        'endMb',
        'graphWidth',
        'lrsMax',
        'additiveCheck',
        'showSNP',
        'showGenes',
        'viewLegend',
        'haplotypeAnalystCheck',
        'mapmethod_rqtl_geno',
        'mapmodel_rqtl_geno',
        'temp_trait',
        'reaper_version',
        'n_samples',
        'transform'
    )
    start_vars = {}
    for key, value in list(initial_start_vars.items()):
        if key in wanted:
            start_vars[key] = value

    version = "v3"
    key = "mapping_results:{}:".format(
        version) + json.dumps(start_vars, sort_keys=True)
    with Bench("Loading cache"):
        result = None  # Just for testing
        #result = Redis.get(key)

    #logger.info("************************ Starting result *****************")
    #logger.info("result is [{}]: {}".format(type(result), result))
    #logger.info("************************ Ending result ********************")

    if result:
        logger.info("Cache hit!!!")
        with Bench("Loading results"):
            result = pickle.loads(result)
    else:
        logger.info("Cache miss!!!")
        with Bench("Total time in RunMapping"):
            try:
                template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
                if template_vars.no_results:
                    rendered_template = render_template("mapping_error.html")
                    return rendered_template
            except:
                rendered_template = render_template("mapping_error.html")
                return rendered_template

            template_vars.js_data = json.dumps(template_vars.js_data,
                                               default=json_default_handler,
                                               indent="   ")

            result = template_vars.__dict__

            if result['pair_scan']:
                with Bench("Rendering template"):
                    img_path = result['pair_scan_filename']
                    logger.info("img_path:", img_path)
                    initial_start_vars = request.form
                    logger.info("initial_start_vars:", initial_start_vars)
                    imgfile = open(TEMPDIR + img_path, 'rb')
                    imgdata = imgfile.read()
                    imgB64 = base64.b64encode(imgdata)
                    bytesarray = array.array('B', imgB64)
                    result['pair_scan_array'] = bytesarray
                    rendered_template = render_template(
                        "pair_scan_results.html", **result)
            else:
                gn1_template_vars = display_mapping_results.DisplayMappingResults(
                    result).__dict__

                with Bench("Rendering template"):
                    rendered_template = render_template(
                        "mapping_results.html", **gn1_template_vars)

    return rendered_template


@app.route("/export_mapping_results", methods=('POST',))
def export_mapping_results():
    logger.info("request.form:", request.form)
    logger.info(request.url)
    file_path = request.form.get("results_path")
    results_csv = open(file_path, "r").read()
    response = Response(results_csv,
                        mimetype='text/csv',
                        headers={"Content-Disposition": "attachment;filename=mapping_results.csv"})

    return response


@app.route("/export_corr_matrix", methods=('POST',))
def export_corr_matrix():
    file_path = request.form.get("export_filepath")
    file_name = request.form.get("export_filename")
    results_csv = open(file_path, "r").read()
    response = Response(results_csv,
                        mimetype='text/csv',
                        headers={"Content-Disposition": "attachment;filename=" + file_name + ".csv"})

    return response


@app.route("/export", methods=('POST',))
def export():
    logger.info("request.form:", request.form)
    logger.info(request.url)
    svg_xml = request.form.get("data", "Invalid data")
    filename = request.form.get("filename", "manhattan_plot_snp")
    response = Response(svg_xml, mimetype="image/svg+xml")
    response.headers["Content-Disposition"] = "attachment; filename=%s" % filename
    return response


@app.route("/export_pdf", methods=('POST',))
def export_pdf():
    import cairosvg
    logger.info("request.form:", request.form)
    logger.info(request.url)
    svg_xml = request.form.get("data", "Invalid data")
    logger.info("svg_xml:", svg_xml)
    filename = request.form.get("filename", "interval_map_pdf")
    pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
    response = Response(pdf_file, mimetype="application/pdf")
    response.headers["Content-Disposition"] = "attachment; filename=%s" % filename
    return response


@app.route("/network_graph", methods=('POST',))
def network_graph_page():
    logger.info("In network_graph, request.form is:", pf(request.form))
    logger.info(request.url)
    start_vars = request.form
    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
    if traits[0] != "":
        template_vars = network_graph.NetworkGraph(start_vars)
        template_vars.js_data = json.dumps(template_vars.js_data,
                                           default=json_default_handler,
                                           indent="   ")

        return render_template("network_graph.html", **template_vars.__dict__)
    else:
        return render_template("empty_collection.html", **{'tool': 'Network Graph'})


@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
    logger.info("In corr_compute, request.form is:", pf(request.form))
    logger.info(request.url)
    template_vars = show_corr_results.CorrelationResults(request.form)
    return render_template("correlation_page.html", **template_vars.__dict__)

    # to test/disable the new  correlation api uncomment these lines

    # correlation_results = compute_correlation(request.form)
    # return render_template("test_correlation_page.html", correlation_results=correlation_results)


@app.route("/test_corr_compute", methods=["POST"])
def test_corr_compute_page():
    correlation_data = compute_correlation(request.form)
    return render_template("test_correlation_page.html", **correlation_data)
    
@app.route("/corr_matrix", methods=('POST',))
def corr_matrix_page():
    logger.info("In corr_matrix, request.form is:", pf(request.form))
    logger.info(request.url)

    start_vars = request.form
    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
    if len(traits) > 1:
        template_vars = show_corr_matrix.CorrelationMatrix(start_vars)
        template_vars.js_data = json.dumps(template_vars.js_data,
                                           default=json_default_handler,
                                           indent="   ")

        return render_template("correlation_matrix.html", **template_vars.__dict__)
    else:
        return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'})


@app.route("/corr_scatter_plot")
def corr_scatter_plot_page():
    logger.info(request.url)
    template_vars = corr_scatter_plot.CorrScatterPlot(request.args)
    template_vars.js_data = json.dumps(template_vars.js_data,
                                       default=json_default_handler,
                                       indent="   ")
    return render_template("corr_scatterplot.html", **template_vars.__dict__)


@app.route("/snp_browser", methods=('GET',))
def snp_browser_page():
    logger.info(request.url)
    template_vars = snp_browser.SnpBrowser(request.args)

    return render_template("snp_browser.html", **template_vars.__dict__)


@app.route("/db_info", methods=('GET',))
def db_info_page():
    template_vars = InfoPage(request.args)

    return render_template("info_page.html", **template_vars.__dict__)


@app.route("/snp_browser_table", methods=('GET',))
def snp_browser_table():
    logger.info(request.url)
    snp_table_data = snp_browser.SnpBrowser(request.args)
    current_page = server_side.ServerSideTable(
        snp_table_data.rows_count,
        snp_table_data.table_rows,
        snp_table_data.header_data_names,
        request.args,
    ).get_page()

    return flask.jsonify(current_page)


@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
    # ZS: Currently just links to GN1
    logger.info(request.url)
    return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")


@app.route("/tutorial/security", methods=('GET',))
def security_tutorial_page():
    # ZS: Currently just links to GN1
    logger.info(request.url)
    return render_template("admin/security_help.html")


@app.route("/submit_bnw", methods=('POST',))
def submit_bnw():
    logger.info(request.url)
    return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'})

# Take this out or secure it before putting into production


@app.route("/get_temp_data")
def get_temp_data():
    logger.info(request.url)
    temp_uuid = request.args['key']
    return flask.jsonify(temp_data.TempData(temp_uuid).get_all())


@app.route("/browser_input", methods=('GET',))
def browser_inputs():
    """  Returns JSON from tmp directory for the purescript genome browser"""

    filename = request.args['filename']

    with open("{}/gn2/".format(TEMPDIR) + filename + ".json", "r") as the_file:
        file_contents = json.load(the_file)

    return flask.jsonify(file_contents)

##########################################################################


def json_default_handler(obj):
    """Based on http://stackoverflow.com/a/2680060/1175849"""
    # Handle datestamps
    if hasattr(obj, 'isoformat'):
        return obj.isoformat()
    # Handle integer keys for dictionaries
    elif isinstance(obj, int) or isinstance(obj, uuid.UUID):
        return str(obj)
    # Handle custom objects
    if hasattr(obj, '__dict__'):
        return obj.__dict__
    else:
        raise TypeError('Object of type %s with value of %s is not JSON serializable' % (
            type(obj), repr(obj)))