serializers.py

from rest_framework import serializers
from genes.serializers import GeneGEMWithType
from user_files.models_choices import MoleculeType
from .models import Biomarker, MRNAIdentifier, MethylationIdentifier, CNAIdentifier, MiRNAIdentifier, MoleculeIdentifier
from tags.serializers import TagSerializer
from drf_writable_nested import WritableNestedModelSerializer


class MoleculeIdentifierSerializer(serializers.Serializer):
    """
    Serializer for all the types of molecules (MRNAIdentifier, MiRNAIdentifier, CNAIdentifier, or
    MethylationIdentifier). Gets their ID and identifier only.
    """
    id = serializers.IntegerField()
    identifier = serializers.CharField()
    type = serializers.SerializerMethodField(method_name='get_type')

    @staticmethod
    def get_type(instance: MoleculeIdentifier) -> MoleculeType:
        if isinstance(instance, MRNAIdentifier):
            return MoleculeType.MRNA
        if isinstance(instance, MiRNAIdentifier):
            return MoleculeType.MIRNA
        if isinstance(instance, CNAIdentifier):
            return MoleculeType.CNA
        return MoleculeType.METHYLATION


class MRNAIdentifierSerializer(serializers.ModelSerializer):
    """MRNAIdentifier serializer"""

    class Meta:
        model = MRNAIdentifier
        exclude = ['biomarker']


class MiRNAIdentifierSerializer(serializers.ModelSerializer):
    """MiRNAIdentifier serializer"""

    class Meta:
        model = MiRNAIdentifier
        exclude = ['biomarker']


class CNAIdentifierSerializer(serializers.ModelSerializer):
    """CNAIdentifier serializer"""

    class Meta:
        model = CNAIdentifier
        exclude = ['biomarker']


class MethylationIdentifierSerializer(serializers.ModelSerializer):
    """MethylationIdentifier serializer"""

    class Meta:
        model = MethylationIdentifier
        exclude = ['biomarker']


class BiomarkerSimpleSerializer(WritableNestedModelSerializer):
    """Biomarker model serializer without the molecules (useful to list Biomarkers)."""
    number_of_mrnas = serializers.SerializerMethodField(method_name='get_number_of_mrnas')
    number_of_mirnas = serializers.SerializerMethodField(method_name='get_number_of_mirnas')
    number_of_cnas = serializers.SerializerMethodField(method_name='get_number_of_cnas')
    number_of_methylations = serializers.SerializerMethodField(method_name='get_number_of_methylations')
    has_fs_experiment = serializers.SerializerMethodField(method_name='get_has_fs_experiment')

    origin = serializers.IntegerField(required=False)
    state = serializers.IntegerField(required=False)

    tag = TagSerializer(required=False)

    class Meta:
        model = Biomarker
        exclude = ['user']

    @staticmethod
    def get_number_of_mrnas(ins: Biomarker) -> int:
        """Gets the number of genes in this Biomarker"""
        return ins.number_of_mrnas

    @staticmethod
    def get_number_of_mirnas(ins: Biomarker) -> int:
        """Gets the number of miRNAs in this Biomarker"""
        return ins.number_of_mirnas

    @staticmethod
    def get_number_of_cnas(ins: Biomarker) -> int:
        """Gets the number of CNAs in this Biomarker"""
        return ins.number_of_cnas

    @staticmethod
    def get_number_of_methylations(ins: Biomarker) -> int:
        """Gets the number of Methylations in this Biomarker"""
        return ins.number_of_methylations

    @staticmethod
    def get_has_fs_experiment(ins: Biomarker) -> bool:
        """Gets if the current Biomarker was created from a Feature Selection experiment"""
        return ins.has_fs_experiment


class BiomarkerSimpleUpdateSerializer(serializers.ModelSerializer):
    """
    This serializer is used to update only the name and description of the Biomarker model to prevent updating all
    the molecules when it's not necessary.
    """
    class Meta:
        model = Biomarker
        fields = ['name', 'description']


class BiomarkerSerializer(WritableNestedModelSerializer):
    """Biomarker model serializer (useful to create/edit a Biomarker)."""
    number_of_mrnas = serializers.SerializerMethodField(method_name='get_number_of_mrnas')
    number_of_mirnas = serializers.SerializerMethodField(method_name='get_number_of_mirnas')
    number_of_cnas = serializers.SerializerMethodField(method_name='get_number_of_cnas')
    number_of_methylations = serializers.SerializerMethodField(method_name='get_number_of_methylations')
    has_fs_experiment = serializers.SerializerMethodField(method_name='get_has_fs_experiment')
    was_already_used = serializers.SerializerMethodField(method_name='get_was_already_used')

    mrnas = MRNAIdentifierSerializer(many=True, required=False)
    mirnas = MiRNAIdentifierSerializer(many=True, required=False)
    cnas = CNAIdentifierSerializer(many=True, required=False)
    methylations = MethylationIdentifierSerializer(many=True, required=False)
    origin = serializers.IntegerField(required=False)
    state = serializers.IntegerField(required=False)

    tag = TagSerializer(required=False)

    class Meta:
        model = Biomarker
        exclude = ['user']

    @staticmethod
    def get_number_of_mrnas(ins: Biomarker) -> int:
        """Gets the number of genes in this Biomarker"""
        return ins.number_of_mrnas

    @staticmethod
    def get_number_of_mirnas(ins: Biomarker) -> int:
        """Gets the number of miRNAs in this Biomarker"""
        return ins.number_of_mirnas

    @staticmethod
    def get_number_of_cnas(ins: Biomarker) -> int:
        """Gets the number of CNAs in this Biomarker"""
        return ins.number_of_cnas

    @staticmethod
    def get_number_of_methylations(ins: Biomarker) -> int:
        """Gets the number of Methylations in this Biomarker"""
        return ins.number_of_methylations

    @staticmethod
    def get_has_fs_experiment(ins: Biomarker) -> bool:
        """Gets if the current Biomarker was created from a Feature Selection experiment"""
        return ins.has_fs_experiment

    @staticmethod
    def get_was_already_used(ins: Biomarker) -> bool:
        """
        Returns True if this Biomarker was used for an Inference experiment, Statistical Validation or Trained Model.
        This avoids the user to edit a Biomarker that was already used and generate inconsistencies.
        """
        return ins.was_already_used
    
    
class BiomarkerFromCorrelationAnalysisSerializer(serializers.Serializer):
    """
    Serializer for BiomarkerFromCorrelationAnalysis, including correlation analysis ID, gene GEM list, and correlation threshold.
    """
    correlation_analysis_id = serializers.IntegerField()
    gene_gem_list = GeneGEMWithType(many=True, required=False)
    correlation_threshold = serializers.IntegerField(required=False)