from openomics.database.annotation import GTEx

from openomics.database.ontology import GeneOntology

from openomics.database.sequence import RNAcentral

from .test_multiomics import *

@pytest.fixture

def generate_RNACentral_ftp():

    rnacentral = RNAcentral(path="https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/")

    rnacentral.data = rnacentral.data.sample(frac=0.01)

    return rnacentral

@pytest.fixture

def generate_GTEx_expressions():

    return GTEx(path="https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/", )

@pytest.fixture

def generate_GeneOntology():

    go = GeneOntology(path="http://geneontology.org/gene-associations/", species='human')

    go.data = go.data.sample(frac=0.01)

    return go

def test_import_rnacentral_db(generate_RNACentral_ftp):

    assert generate_RNACentral_ftp.data_path == 'https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/'

def test_import_GTEx(generate_GTEx_expressions):

    assert generate_GTEx_expressions.data_path == "https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/"

    assert not generate_GTEx_expressions.get_expressions(index="gene_name").empty

    assert not generate_GTEx_expressions.get_expressions(index="gene_id").empty

def test_import_GeneOntology(generate_GeneOntology):

    assert generate_GeneOntology.data_path == "http://geneontology.org/gene-associations/"

def test_annotate_rnacentral(generate_TCGA_LUAD, generate_RNACentral_ftp):

    generate_TCGA_LUAD.MicroRNA.annotate_attributes(database=generate_RNACentral_ftp,

                                                    on="gene_name",

                                                    columns=['gene_name', 'RNA type'])

    assert {'RNA type'}.issubset(generate_TCGA_LUAD.MicroRNA.annotations.columns)

def test_annotate_expressions_GTEx(generate_TCGA_LUAD, generate_GTEx_expressions):

    generate_TCGA_LUAD.LncRNA.annotate_expressions(database=generate_GTEx_expressions, index="gene_id")

    assert not generate_TCGA_LUAD.LncRNA.get_annotation_expressions().empty

def test_annotate_GeneOntology(generate_TCGA_LUAD, generate_GeneOntology):

    generate_TCGA_LUAD.MessengerRNA.annotate_attributes(database=generate_GeneOntology, on="gene_name",

                                                        columns=['go_id'])

    assert {'go_id'}.issubset(generate_TCGA_LUAD.MessengerRNA.annotations.columns)

    assert not generate_TCGA_LUAD.MessengerRNA.annotations["go_id"].empty