bar_utils.py

import re
import redis
import os


class BARUtils:
    @staticmethod
    def error_exit(msg):
        """Exit if failed
        :param msg: message to pass on failure
        :return:
        """
        result = {"wasSuccessful": False, "error": msg}
        return result

    @staticmethod
    def success_exit(msg):
        """Output if success
        :param msg: the actual data the needs to be output
        :return:
        """
        result = {"wasSuccessful": True, "data": msg}
        return result

    @staticmethod
    def is_arabidopsis_gene_valid(gene):
        """This function verifies if Arabidopsis gene is valid
        :param gene:
        :return:
        """
        if re.search(r"^At[12345cm]g\d{5}.?\d?$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_grape_gene_valid(gene):
        """This function verifies if grape gene is valid: VIT_00s0120g00060
        :param gene:
        :return:
        """
        if re.search(r"^VIT_\d{0,3}\D\d{0,5}g\d{0,6}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_poplar_gene_valid(gene):
        """This function verifies if Poplar v3 gene is valid
        :param gene:
        :return: True if valid
        """
        if re.search(r"^POTRI\.\d{3}g\d{6}.?\d{0,3}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_rice_gene_valid(gene, isoform_id=False):
        """This function verifies if rice gene is valid
        :param gene:
        :param isoform_id: True if you want to verifiy isoform ID
        :return: True if valid
        """
        if isoform_id and re.search(r"^LOC_Os\d{2}g\d{5}\.\d{1,2}$", gene, re.I):
            return True
        elif isoform_id is False and re.search(r"^LOC_Os\d{2}g\d{5}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_tomato_gene_valid(gene, isoform_id=False):
        """This function verifies if ITAG Solyc gene is valid
        :param gene:
        :param isoform_id: True if you want to verifiy isoform ID
        :return: True if valid
        """
        if isoform_id and re.search(r"^Solyc\d\dg\d{6}\.\d\.\d$", gene, re.I):
            return True
        elif isoform_id is False and re.search(r"^Solyc\d\dg\d{6}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_cannabis_gene_valid(gene):
        """This function verifies if cannabis gene is valid: AGQN03000001
        :param gene:
        :return: True if valid
        """
        if gene and re.search(r"^AGQN\d{0,10}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_canola_gene_valid(gene):
        """This function verifies if canola gene (BnaC07g42830D) is valid
        :param gene:
        :return:
        """
        if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_arachis_gene_valid(gene):
        """This function verifies if arachis gene is valid: Adur10000_comp0_c0_seq1
        :param gene:
        :return: True if valid
        """
        if gene and re.search(r"^Adur\d{1,10}_comp\d{1,3}_\D{1,3}\d{1,3}_seq\d{1,5}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_brassica_rapa_gene_valid(gene):
        """This function verifies if Brassica rapa gene is valid: BraA01g000010
        :param gene:
        :return: True if valid
        """
        if gene and re.search(r"^BraA.{1,4}g\d{1,9}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_soybean_gene_valid(gene):
        """This function verifies if soybean gene is valid: Glyma06g47400
        :param gene:
        :return: True if valid
        """
        if gene and re.search(r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)|(Glyma\.\d{1,3}g\d{1,8}))$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_maize_gene_valid(gene):
        """This function verifies if maize gene is valid: Zm00001d046170
        :param gene:
        :return: True if valid
        """
        if gene and re.search(
            r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})|(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})|(GRMZM(2|5)G[0-9]{6})|(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})|(Zm\d+d\d+)$",
            gene,
            re.I,
        ):
            return True
        else:
            return False

    @staticmethod
    def is_sorghum_gene_valid(gene):
        """This function verifies if Arabidopsis gene is valid
        :param gene:
        :return:
        """
        if re.search(r"^(Sobic.\d{0,5}G\d{0,10}|Sobic.K\d{0,10})$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_kalanchoe_gene_valid(gene):
        """This function verifies if Kalanchoe gene is valid
        :param gene:
        :return:
        """
        if re.search(r"^Kaladp\d{1,10}s\d{1,10}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_phelipanche_gene_valid(gene):
        """This function verifies if phelipanche gene (OrAeBC5_9992.10) is valid
        :param gene:
        :return:
        """
        if re.search(r"^OrAeBC5_\d{1,6}\.\d{1,3}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_physcomitrella_gene_valid(gene):
        """This function verifies if physcomitrella gene (Pp1s9_70V6.1) is valid
        :param gene:
        :return:
        """
        if re.search(r"^Pp1s\d{1,8}_\d{1,8}V6\.\d{1,3}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_selaginella_gene_valid(gene):
        """This function verifies if selaginella gene (Smo402070) is valid
        :param gene:
        :return:
        """
        if re.search(r"^Smo\d{1,8}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_strawberry_gene_valid(gene):
        """This function verifies if strawberry gene (FvH4_1g00010) is valid
        :param gene:
        :return:
        """
        if re.search(r"^FvH4_\d{1,3}g\d{1,8}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_striga_gene_valid(gene):
        """This function verifies if striga gene (StHeBC3_9993.10) is valid
        :param gene:
        :return:
        """
        if re.search(r"^StHeBC3_\d{1,6}\.\d{1,5}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_triphysaria_gene_valid(gene):
        """This function verifies if triphysaria gene (TrVeBC3_9999.18) is valid
        :param gene:
        :return:
        """
        if re.search(r"^TrVeBC3_\d{1,6}\.\d{1,3}$", gene, re.I):
            return True
        else:
            return False

    @staticmethod
    def is_integer(data):
        """Check if the input is at max ten figure number.
        :param data: int number
        :return: True if a number
        """
        if re.search(r"^\d{1,10}$", data):
            return True
        else:
            return False

    @staticmethod
    def is_gaia_alias(data):
        """Check if the input is a valid gaia alias.
        :param data
        :return: True if valid gaia alias
        """
        if re.search(r"^[a-z0-9_]{1,50}$", data, re.I):
            return True
        else:
            return False

    @staticmethod
    def format_poplar(poplar_gene):
        """Format Poplar gene ID to be Potri.016G107900, i.e. capitalized P and G
        :param poplar_gene: gene id
        :return: String
        """
        return poplar_gene.translate(str.maketrans("pOTRIg", "PotriG"))

    @staticmethod
    def connect_redis():
        """This function connects to redis
        :returns: redis connection
        """
        if os.environ.get("BAR"):
            r = redis.Redis(
                host=os.environ.get("BAR_REDIS_HOST"), port=6379, password=os.environ.get("BAR_REDIS_PASSWORD")
            )
        else:
            r = redis.Redis(host="localhost")

        return r