"""This module provides methods for handling queries."""
from typing import Tuple, Optional, List
from gene.query import QueryHandler as GeneQueryHandler
from ga4gh.vrs.dataproxy import SeqRepoDataProxy
from ga4gh.vrs.extras.translator import Translator
from variation import SEQREPO_DATA_PATH, TRANSCRIPT_MAPPINGS_PATH, \
    REFSEQ_GENE_SYMBOL_PATH, AMINO_ACID_PATH, UTA_DB_URL, REFSEQ_MANE_PATH
from variation.schemas.ga4gh_vrsatile import VariationDescriptor
from variation.to_vrs import ToVRS
from variation.normalize import Normalize
from variation.classifiers import Classify
from variation.tokenizers import Tokenize
from variation.validators import Validate
from variation.translators import Translate
from variation.data_sources import SeqRepoAccess, TranscriptMappings, \
    UTA, MANETranscriptMappings
from variation.mane_transcript import MANETranscript
from variation.tokenizers import GeneSymbol
from variation.tokenizers.caches import AminoAcidCache
from variation.schemas.ga4gh_vrs import Text, Allele


class QueryHandler:
    """Class for handling queries."""

    def __init__(self,
                 dynamodb_url: str = '',
                 dynamodb_region: str = 'us-east-2',
                 seqrepo_data_path=SEQREPO_DATA_PATH,
                 uta_db_url=UTA_DB_URL,
                 uta_db_pwd=None) -> None:
        """Initialize QueryHandler instance.
        :param str dynamodb_url: URL to gene-normalizer database source.
        :param str dynamodb_region: AWS default region for gene-normalizer.
        :param str seqrepo_data_path: Path to seqrepo data directory
        :param str uta_db_url: URL for UTA database
        :param str uta_db_pwd: Password for UTA database user
        """
        self.gene_normalizer = GeneQueryHandler(db_url=dynamodb_url,
                                                db_region=dynamodb_region)
        self.seqrepo_access = SeqRepoAccess(
            seqrepo_data_path=seqrepo_data_path
        )
        self.uta = UTA(db_url=uta_db_url, db_pwd=uta_db_pwd)
        self.to_vrs_handler = self._init_to_vrs()
        self.normalize_handler = Normalize(
            self.seqrepo_access, self.uta, self.gene_normalizer
        )

    def _init_to_vrs(self, transcript_file_path=TRANSCRIPT_MAPPINGS_PATH,
                     refseq_file_path=REFSEQ_GENE_SYMBOL_PATH,
                     amino_acids_file_path=AMINO_ACID_PATH,
                     mane_data_path=REFSEQ_MANE_PATH) -> ToVRS:
        """Return toVRS instance

        :param str transcript_file_path: Path to transcript mappings file
        :param str refseq_file_path: Path to refseq gene symbol file
        :param str amino_acids_file_path: Path to amino acids file
        :param str mane_data_path: Path to refseq mane data file
        :return: toVRS instance
        """
        gene_symbol = GeneSymbol(self.gene_normalizer)
        amino_acid_cache = AminoAcidCache(
            amino_acids_file_path=amino_acids_file_path
        )
        tokenizer = Tokenize(amino_acid_cache, gene_symbol)
        classifier = Classify()
        transcript_mappings = TranscriptMappings(
            transcript_file_path=transcript_file_path,
            refseq_file_path=refseq_file_path
        )
        mane_transcript_mappings = MANETranscriptMappings(
            mane_data_path=mane_data_path
        )
        dp = SeqRepoDataProxy(self.seqrepo_access.seq_repo_client)
        tlr = Translator(data_proxy=dp)
        mane_transcript = MANETranscript(
            self.seqrepo_access, transcript_mappings,
            mane_transcript_mappings, self.uta
        )
        validator = Validate(
            self.seqrepo_access, transcript_mappings, gene_symbol,
            mane_transcript, self.uta, dp, tlr, amino_acid_cache
        )
        translator = Translate()
        return ToVRS(
            tokenizer, classifier, self.seqrepo_access, transcript_mappings,
            gene_symbol, amino_acid_cache, self.uta, mane_transcript_mappings,
            mane_transcript, validator, translator
        )

    def to_vrs(self, q) -> Tuple[Optional[List[Allele]], Optional[List[str]]]:
        """Return a VRS-like representation of all validated variations for a query.  # noqa: E501

        :param str q: The variation to translate
        :return: Validated VRS Variations and list of warnings
        """
        validations, warnings = \
            self.to_vrs_handler.get_validations(q)
        translations, warnings = \
            self.to_vrs_handler.get_translations(validations, warnings)

        if not translations:
            if q and q.strip():
                translations = [Text(definition=q)]
            else:
                translations = None
        return translations, warnings

    def normalize(self, q) -> VariationDescriptor:
        """Return normalized Variation Descriptor for variation.

        :param q: Variation to normalize
        :return: Variation Descriptor for variation
        """
        validations, warnings = \
            self.to_vrs_handler.get_validations(q, normalize_endpoint=True)
        return self.normalize_handler.normalize(q, validations, warnings)

e22a95ba093355704f412a3f9d4c1ee65e58172b
<mask token>


class QueryHandler:
    <mask token>
    <mask token>
    <mask token>

    def to_vrs(self, q) ->Tuple[Optional[List[Allele]], Optional[List[str]]]:
        """Return a VRS-like representation of all validated variations for a query.  # noqa: E501

        :param str q: The variation to translate
        :return: Validated VRS Variations and list of warnings
        """
        validations, warnings = self.to_vrs_handler.get_validations(q)
        translations, warnings = self.to_vrs_handler.get_translations(
            validations, warnings)
        if not translations:
            if q and q.strip():
                translations = [Text(definition=q)]
            else:
                translations = None
        return translations, warnings

    def normalize(self, q) ->VariationDescriptor:
        """Return normalized Variation Descriptor for variation.

        :param q: Variation to normalize
        :return: Variation Descriptor for variation
        """
        validations, warnings = self.to_vrs_handler.get_validations(q,
            normalize_endpoint=True)
        return self.normalize_handler.normalize(q, validations, warnings)

<mask token>


class QueryHandler:
    <mask token>
    <mask token>

    def _init_to_vrs(self, transcript_file_path=TRANSCRIPT_MAPPINGS_PATH,
        refseq_file_path=REFSEQ_GENE_SYMBOL_PATH, amino_acids_file_path=
        AMINO_ACID_PATH, mane_data_path=REFSEQ_MANE_PATH) ->ToVRS:
        """Return toVRS instance

        :param str transcript_file_path: Path to transcript mappings file
        :param str refseq_file_path: Path to refseq gene symbol file
        :param str amino_acids_file_path: Path to amino acids file
        :param str mane_data_path: Path to refseq mane data file
        :return: toVRS instance
        """
        gene_symbol = GeneSymbol(self.gene_normalizer)
        amino_acid_cache = AminoAcidCache(amino_acids_file_path=
            amino_acids_file_path)
        tokenizer = Tokenize(amino_acid_cache, gene_symbol)
        classifier = Classify()
        transcript_mappings = TranscriptMappings(transcript_file_path=
            transcript_file_path, refseq_file_path=refseq_file_path)
        mane_transcript_mappings = MANETranscriptMappings(mane_data_path=
            mane_data_path)
        dp = SeqRepoDataProxy(self.seqrepo_access.seq_repo_client)
        tlr = Translator(data_proxy=dp)
        mane_transcript = MANETranscript(self.seqrepo_access,
            transcript_mappings, mane_transcript_mappings, self.uta)
        validator = Validate(self.seqrepo_access, transcript_mappings,
            gene_symbol, mane_transcript, self.uta, dp, tlr, amino_acid_cache)
        translator = Translate()
        return ToVRS(tokenizer, classifier, self.seqrepo_access,
            transcript_mappings, gene_symbol, amino_acid_cache, self.uta,
            mane_transcript_mappings, mane_transcript, validator, translator)

    def to_vrs(self, q) ->Tuple[Optional[List[Allele]], Optional[List[str]]]:
        """Return a VRS-like representation of all validated variations for a query.  # noqa: E501

        :param str q: The variation to translate
        :return: Validated VRS Variations and list of warnings
        """
        validations, warnings = self.to_vrs_handler.get_validations(q)
        translations, warnings = self.to_vrs_handler.get_translations(
            validations, warnings)
        if not translations:
            if q and q.strip():
                translations = [Text(definition=q)]
            else:
                translations = None
        return translations, warnings

    def normalize(self, q) ->VariationDescriptor:
        """Return normalized Variation Descriptor for variation.

        :param q: Variation to normalize
        :return: Variation Descriptor for variation
        """
        validations, warnings = self.to_vrs_handler.get_validations(q,
            normalize_endpoint=True)
        return self.normalize_handler.normalize(q, validations, warnings)

<mask token>


class QueryHandler:
    """Class for handling queries."""

    def __init__(self, dynamodb_url: str='', dynamodb_region: str=
        'us-east-2', seqrepo_data_path=SEQREPO_DATA_PATH, uta_db_url=
        UTA_DB_URL, uta_db_pwd=None) ->None:
        """Initialize QueryHandler instance.
        :param str dynamodb_url: URL to gene-normalizer database source.
        :param str dynamodb_region: AWS default region for gene-normalizer.
        :param str seqrepo_data_path: Path to seqrepo data directory
        :param str uta_db_url: URL for UTA database
        :param str uta_db_pwd: Password for UTA database user
        """
        self.gene_normalizer = GeneQueryHandler(db_url=dynamodb_url,
            db_region=dynamodb_region)
        self.seqrepo_access = SeqRepoAccess(seqrepo_data_path=seqrepo_data_path
            )
        self.uta = UTA(db_url=uta_db_url, db_pwd=uta_db_pwd)
        self.to_vrs_handler = self._init_to_vrs()
        self.normalize_handler = Normalize(self.seqrepo_access, self.uta,
            self.gene_normalizer)

    def _init_to_vrs(self, transcript_file_path=TRANSCRIPT_MAPPINGS_PATH,
        refseq_file_path=REFSEQ_GENE_SYMBOL_PATH, amino_acids_file_path=
        AMINO_ACID_PATH, mane_data_path=REFSEQ_MANE_PATH) ->ToVRS:
        """Return toVRS instance

        :param str transcript_file_path: Path to transcript mappings file
        :param str refseq_file_path: Path to refseq gene symbol file
        :param str amino_acids_file_path: Path to amino acids file
        :param str mane_data_path: Path to refseq mane data file
        :return: toVRS instance
        """
        gene_symbol = GeneSymbol(self.gene_normalizer)
        amino_acid_cache = AminoAcidCache(amino_acids_file_path=
            amino_acids_file_path)
        tokenizer = Tokenize(amino_acid_cache, gene_symbol)
        classifier = Classify()
        transcript_mappings = TranscriptMappings(transcript_file_path=
            transcript_file_path, refseq_file_path=refseq_file_path)
        mane_transcript_mappings = MANETranscriptMappings(mane_data_path=
            mane_data_path)
        dp = SeqRepoDataProxy(self.seqrepo_access.seq_repo_client)
        tlr = Translator(data_proxy=dp)
        mane_transcript = MANETranscript(self.seqrepo_access,
            transcript_mappings, mane_transcript_mappings, self.uta)
        validator = Validate(self.seqrepo_access, transcript_mappings,
            gene_symbol, mane_transcript, self.uta, dp, tlr, amino_acid_cache)
        translator = Translate()
        return ToVRS(tokenizer, classifier, self.seqrepo_access,
            transcript_mappings, gene_symbol, amino_acid_cache, self.uta,
            mane_transcript_mappings, mane_transcript, validator, translator)

    def to_vrs(self, q) ->Tuple[Optional[List[Allele]], Optional[List[str]]]:
        """Return a VRS-like representation of all validated variations for a query.  # noqa: E501

        :param str q: The variation to translate
        :return: Validated VRS Variations and list of warnings
        """
        validations, warnings = self.to_vrs_handler.get_validations(q)
        translations, warnings = self.to_vrs_handler.get_translations(
            validations, warnings)
        if not translations:
            if q and q.strip():
                translations = [Text(definition=q)]
            else:
                translations = None
        return translations, warnings

    def normalize(self, q) ->VariationDescriptor:
        """Return normalized Variation Descriptor for variation.

        :param q: Variation to normalize
        :return: Variation Descriptor for variation
        """
        validations, warnings = self.to_vrs_handler.get_validations(q,
            normalize_endpoint=True)
        return self.normalize_handler.normalize(q, validations, warnings)

<mask token>
from typing import Tuple, Optional, List
from gene.query import QueryHandler as GeneQueryHandler
from ga4gh.vrs.dataproxy import SeqRepoDataProxy
from ga4gh.vrs.extras.translator import Translator
from variation import SEQREPO_DATA_PATH, TRANSCRIPT_MAPPINGS_PATH, REFSEQ_GENE_SYMBOL_PATH, AMINO_ACID_PATH, UTA_DB_URL, REFSEQ_MANE_PATH
from variation.schemas.ga4gh_vrsatile import VariationDescriptor
from variation.to_vrs import ToVRS
from variation.normalize import Normalize
from variation.classifiers import Classify
from variation.tokenizers import Tokenize
from variation.validators import Validate
from variation.translators import Translate
from variation.data_sources import SeqRepoAccess, TranscriptMappings, UTA, MANETranscriptMappings
from variation.mane_transcript import MANETranscript
from variation.tokenizers import GeneSymbol
from variation.tokenizers.caches import AminoAcidCache
from variation.schemas.ga4gh_vrs import Text, Allele


class QueryHandler:
    """Class for handling queries."""

    def __init__(self, dynamodb_url: str='', dynamodb_region: str=
        'us-east-2', seqrepo_data_path=SEQREPO_DATA_PATH, uta_db_url=
        UTA_DB_URL, uta_db_pwd=None) ->None:
        """Initialize QueryHandler instance.
        :param str dynamodb_url: URL to gene-normalizer database source.
        :param str dynamodb_region: AWS default region for gene-normalizer.
        :param str seqrepo_data_path: Path to seqrepo data directory
        :param str uta_db_url: URL for UTA database
        :param str uta_db_pwd: Password for UTA database user
        """
        self.gene_normalizer = GeneQueryHandler(db_url=dynamodb_url,
            db_region=dynamodb_region)
        self.seqrepo_access = SeqRepoAccess(seqrepo_data_path=seqrepo_data_path
            )
        self.uta = UTA(db_url=uta_db_url, db_pwd=uta_db_pwd)
        self.to_vrs_handler = self._init_to_vrs()
        self.normalize_handler = Normalize(self.seqrepo_access, self.uta,
            self.gene_normalizer)

    def _init_to_vrs(self, transcript_file_path=TRANSCRIPT_MAPPINGS_PATH,
        refseq_file_path=REFSEQ_GENE_SYMBOL_PATH, amino_acids_file_path=
        AMINO_ACID_PATH, mane_data_path=REFSEQ_MANE_PATH) ->ToVRS:
        """Return toVRS instance

        :param str transcript_file_path: Path to transcript mappings file
        :param str refseq_file_path: Path to refseq gene symbol file
        :param str amino_acids_file_path: Path to amino acids file
        :param str mane_data_path: Path to refseq mane data file
        :return: toVRS instance
        """
        gene_symbol = GeneSymbol(self.gene_normalizer)
        amino_acid_cache = AminoAcidCache(amino_acids_file_path=
            amino_acids_file_path)
        tokenizer = Tokenize(amino_acid_cache, gene_symbol)
        classifier = Classify()
        transcript_mappings = TranscriptMappings(transcript_file_path=
            transcript_file_path, refseq_file_path=refseq_file_path)
        mane_transcript_mappings = MANETranscriptMappings(mane_data_path=
            mane_data_path)
        dp = SeqRepoDataProxy(self.seqrepo_access.seq_repo_client)
        tlr = Translator(data_proxy=dp)
        mane_transcript = MANETranscript(self.seqrepo_access,
            transcript_mappings, mane_transcript_mappings, self.uta)
        validator = Validate(self.seqrepo_access, transcript_mappings,
            gene_symbol, mane_transcript, self.uta, dp, tlr, amino_acid_cache)
        translator = Translate()
        return ToVRS(tokenizer, classifier, self.seqrepo_access,
            transcript_mappings, gene_symbol, amino_acid_cache, self.uta,
            mane_transcript_mappings, mane_transcript, validator, translator)

    def to_vrs(self, q) ->Tuple[Optional[List[Allele]], Optional[List[str]]]:
        """Return a VRS-like representation of all validated variations for a query.  # noqa: E501

        :param str q: The variation to translate
        :return: Validated VRS Variations and list of warnings
        """
        validations, warnings = self.to_vrs_handler.get_validations(q)
        translations, warnings = self.to_vrs_handler.get_translations(
            validations, warnings)
        if not translations:
            if q and q.strip():
                translations = [Text(definition=q)]
            else:
                translations = None
        return translations, warnings

    def normalize(self, q) ->VariationDescriptor:
        """Return normalized Variation Descriptor for variation.

        :param q: Variation to normalize
        :return: Variation Descriptor for variation
        """
        validations, warnings = self.to_vrs_handler.get_validations(q,
            normalize_endpoint=True)
        return self.normalize_handler.normalize(q, validations, warnings)

"""This module provides methods for handling queries."""
from typing import Tuple, Optional, List
from gene.query import QueryHandler as GeneQueryHandler
from ga4gh.vrs.dataproxy import SeqRepoDataProxy
from ga4gh.vrs.extras.translator import Translator
from variation import SEQREPO_DATA_PATH, TRANSCRIPT_MAPPINGS_PATH, \
    REFSEQ_GENE_SYMBOL_PATH, AMINO_ACID_PATH, UTA_DB_URL, REFSEQ_MANE_PATH
from variation.schemas.ga4gh_vrsatile import VariationDescriptor
from variation.to_vrs import ToVRS
from variation.normalize import Normalize
from variation.classifiers import Classify
from variation.tokenizers import Tokenize
from variation.validators import Validate
from variation.translators import Translate
from variation.data_sources import SeqRepoAccess, TranscriptMappings, \
    UTA, MANETranscriptMappings
from variation.mane_transcript import MANETranscript
from variation.tokenizers import GeneSymbol
from variation.tokenizers.caches import AminoAcidCache
from variation.schemas.ga4gh_vrs import Text, Allele


class QueryHandler:
    """Class for handling queries."""

    def __init__(self,
                 dynamodb_url: str = '',
                 dynamodb_region: str = 'us-east-2',
                 seqrepo_data_path=SEQREPO_DATA_PATH,
                 uta_db_url=UTA_DB_URL,
                 uta_db_pwd=None) -> None:
        """Initialize QueryHandler instance.
        :param str dynamodb_url: URL to gene-normalizer database source.
        :param str dynamodb_region: AWS default region for gene-normalizer.
        :param str seqrepo_data_path: Path to seqrepo data directory
        :param str uta_db_url: URL for UTA database
        :param str uta_db_pwd: Password for UTA database user
        """
        self.gene_normalizer = GeneQueryHandler(db_url=dynamodb_url,
                                                db_region=dynamodb_region)
        self.seqrepo_access = SeqRepoAccess(
            seqrepo_data_path=seqrepo_data_path
        )
        self.uta = UTA(db_url=uta_db_url, db_pwd=uta_db_pwd)
        self.to_vrs_handler = self._init_to_vrs()
        self.normalize_handler = Normalize(
            self.seqrepo_access, self.uta, self.gene_normalizer
        )

    def _init_to_vrs(self, transcript_file_path=TRANSCRIPT_MAPPINGS_PATH,
                     refseq_file_path=REFSEQ_GENE_SYMBOL_PATH,
                     amino_acids_file_path=AMINO_ACID_PATH,
                     mane_data_path=REFSEQ_MANE_PATH) -> ToVRS:
        """Return toVRS instance

        :param str transcript_file_path: Path to transcript mappings file
        :param str refseq_file_path: Path to refseq gene symbol file
        :param str amino_acids_file_path: Path to amino acids file
        :param str mane_data_path: Path to refseq mane data file
        :return: toVRS instance
        """
        gene_symbol = GeneSymbol(self.gene_normalizer)
        amino_acid_cache = AminoAcidCache(
            amino_acids_file_path=amino_acids_file_path
        )
        tokenizer = Tokenize(amino_acid_cache, gene_symbol)
        classifier = Classify()
        transcript_mappings = TranscriptMappings(
            transcript_file_path=transcript_file_path,
            refseq_file_path=refseq_file_path
        )
        mane_transcript_mappings = MANETranscriptMappings(
            mane_data_path=mane_data_path
        )
        dp = SeqRepoDataProxy(self.seqrepo_access.seq_repo_client)
        tlr = Translator(data_proxy=dp)
        mane_transcript = MANETranscript(
            self.seqrepo_access, transcript_mappings,
            mane_transcript_mappings, self.uta
        )
        validator = Validate(
            self.seqrepo_access, transcript_mappings, gene_symbol,
            mane_transcript, self.uta, dp, tlr, amino_acid_cache
        )
        translator = Translate()
        return ToVRS(
            tokenizer, classifier, self.seqrepo_access, transcript_mappings,
            gene_symbol, amino_acid_cache, self.uta, mane_transcript_mappings,
            mane_transcript, validator, translator
        )

    def to_vrs(self, q) -> Tuple[Optional[List[Allele]], Optional[List[str]]]:
        """Return a VRS-like representation of all validated variations for a query.  # noqa: E501

        :param str q: The variation to translate
        :return: Validated VRS Variations and list of warnings
        """
        validations, warnings = \
            self.to_vrs_handler.get_validations(q)
        translations, warnings = \
            self.to_vrs_handler.get_translations(validations, warnings)

        if not translations:
            if q and q.strip():
                translations = [Text(definition=q)]
            else:
                translations = None
        return translations, warnings

    def normalize(self, q) -> VariationDescriptor:
        """Return normalized Variation Descriptor for variation.

        :param q: Variation to normalize
        :return: Variation Descriptor for variation
        """
        validations, warnings = \
            self.to_vrs_handler.get_validations(q, normalize_endpoint=True)
        return self.normalize_handler.normalize(q, validations, warnings)
