new_routes.py

from bottle import request, response, static_file
import hashlib
import os
import pandas as pd
import time

pdApp.tprefix = "iFISH4U|Probe Design|"
pdApp.vd["breadcrumbs"] = True
pdApp.vd["SHOW_COOKIE_CONSENT_BANNER"] = True
pdApp.vd["menu_template"] = "design_menu.tpl"
pdApp.vd["google_analytics_token"] = "UA-99031010-6"


class EnableCors(object):
    """https://stackoverflow.com/a/17262900/1593536"""

    name = "enable_cors"
    api = 2

    def apply(self, fn, context):
        def _enable_cors(*args, **kwargs):
            # set CORS headers
            response.headers["Access-Control-Allow-Origin"] = "*"
            response.headers["Access-Control-Allow-Methods"] = "GET, POST, PUT, OPTIONS"
            response.headers[
                "Access-Control-Allow-Headers"
            ] = "Origin, Accept, Content-Type, X-Requested-With, X-CSRF-Token"
            if request.method != "OPTIONS":
                # actual request; reply with the actual response
                return fn(*args, **kwargs)

        return _enable_cors


pdApp.install(EnableCors())


@root.route("/browse")
@root.route("/browse/")
@bot.view("browse")
def callback():
    d = {}
    d["custom_stylesheets"] = []
    d["title"] = "iFISH4U|Browse"
    d["description"] = "Browse iFISH probes."
    return d


@root.route("/download")
@root.route("/download/")
@bot.view("download")
def callback():
    d = {}
    d["custom_stylesheets"] = []
    d["title"] = "iFISH4U|Download"
    d["description"] = "Download iFISH databases."
    return d


@root.route("/aftf")
@root.route("/aftf/")
@bot.view("aftf")
def callback():
    d = {}
    d["custom_stylesheets"] = []
    d["title"] = "iFISH4U|Advanced FISH Techniques Facility"
    d["description"] = "Order probes via our facility."
    return d


@root.route("/custom_images/<path>")
def callback(path):
    return bot.static_file(path, f"{os.path.dirname(args.custom_routes)}/images/")


@root.route("/custom_css/<path>")
def callback(path):
    return bot.static_file(path, f"{os.path.dirname(args.custom_routes)}/css/")


@root.route("/custom_js/<path>")
def callback(path):
    return bot.static_file(path, f"{os.path.dirname(args.custom_routes)}/js/")


@root.route("/custom_data/<path>")
def callback(path):
    return bot.static_file(path, f"{os.path.dirname(args.custom_routes)}/data/")


@root.route("/custom/giemsa_bands")
def callback():
    giemsa = pd.read_csv(
        os.path.join(
            os.path.dirname(args.custom_routes), "data", "hg19.giemsa_bands.txt"
        ),
        "\t",
    )
    return giemsa.to_json(orient="records")


@root.route("/custom/giemsa_bands/chr/<chrom>")
def callback(chrom):
    giemsa = pd.read_csv(
        os.path.join(
            os.path.dirname(args.custom_routes), "data", "hg19.giemsa_bands.txt"
        ),
        "\t",
    )
    giemsa = giemsa.loc[giemsa["chrom"] == chrom]
    giemsa = giemsa.reset_index()
    return giemsa.to_json(orient="records")


@root.route("/custom/probe_list")
def callback():
    probes = pd.read_csv(
        os.path.join(
            os.path.dirname(args.custom_routes),
            "data",
            "tda_dna-unifish_oligopool_chr_spotting.bed",
        ),
        "\t",
    )
    return probes.to_json(orient="records")


@root.route("/custom/probe_list/pos/<chrom>\:<chromStart>-<chromEnd>")
def callback(chrom, chromStart, chromEnd):
    probes = pd.read_csv(
        os.path.join(
            os.path.dirname(args.custom_routes),
            "data",
            "tda_dna-unifish_oligopool_chr_spotting.bed",
        ),
        "\t",
    )
    probes = probes.loc[probes["chrom"].values == chrom, :]
    probes = probes.loc[probes["chromStart"].values >= int(chromStart), :]
    probes = probes.loc[probes["chromEnd"].values <= int(chromEnd), :]
    return probes.to_json(orient="records")


@root.get("/custom/probe_download/")
def callback():
    GET = dict(request.query)
    probeList = GET["probes"].replace("[", "").replace("]", "").split(",")
    withPrimers = int(GET["primers"]) == 1
    fastaTotal = [""]
    for probeName in probeList:
        probeName = probeName.strip('"')
        if withPrimers:
            probePath = f"{probeName}.with_primers.fa"
        else:
            probePath = f"{probeName}.fa"
        probePath = os.path.join(
            os.path.dirname(args.custom_routes), "data", "probes", probePath
        )
        if not os.path.isfile(probePath):
            return f'ERROR: cannot find probe "{probeName}".'
        else:
            with open(probePath, "r") as IH:
                fastaTotal.append("".join(IH.readlines()))

    encoder = hashlib.sha256()
    encoder.update(bytes(str(time.time()), "utf-8"))
    fastaName = encoder.hexdigest()
    response.set_header("Content-Disposition", f'attachment; filename="{fastaName}.fa"')
    response.set_header("Content-Type", "plain/txt")

    return "".join(fastaTotal).strip()


@root.route("/custom/dbdownload/hg19")
def callback():
    return static_file(
        "iFISH.40mer.tsv.gz",
        os.path.join(os.path.dirname(args.custom_routes), "data", "databases"),
        download="iFISH.40mer.hg19.gz",
        mimetype="application/gzip",
    )


@root.route("/custom/dbdownload/clean/hg19")
def callback():
    return static_file(
        "iFISH.40mer.clean.tsv.gz",
        os.path.join(os.path.dirname(args.custom_routes), "data", "databases"),
        download="iFISH.40mer.hg19.clean.gz",
        mimetype="application/gzip",
    )


@root.route("/custom/dbdownload/chrom/<chrom>")
def callback(chrom):
    return static_file(
        f"{chrom}.gz",
        os.path.join(
            os.path.dirname(args.custom_routes),
            "data",
            "databases",
            "iFISH.40mer.singleChr",
        ),
        download=f"iFISH.40mer.hg19.{chrom}.gz",
        mimetype="application/gzip",
    )


@root.route("/custom/dbdownload/clean/chrom/<chrom>")
def callback(chrom):
    return static_file(
        f"{chrom}.gz",
        os.path.join(
            os.path.dirname(args.custom_routes),
            "data",
            "databases",
            "iFISH.40mer.clean.singleChr",
        ),
        download=f"iFISH.40mer.hg19.clean.{chrom}.gz",
        mimetype="application/gzip",
    )