--- a +++ b/tests/test_disease.py @@ -0,0 +1,88 @@ +from openomics.database.disease import DisGeNet, LncRNADisease, HMDD, MalaCards + +from .test_multiomics import * + + +@pytest.fixture +def generate_DisGeNet_ftp(): + return DisGeNet(path="https://www.disgenet.org/static/disgenet_ap1/files/downloads/", curated=True) + + +@pytest.fixture +def generate_LncRNADisease_ftp(): + return LncRNADisease(path="http://www.cuilab.cn/files/images/ldd/", species="Human") + + +@pytest.fixture +def generate_HMDD_ftp(): + return HMDD(path="http://www.cuilab.cn/static/hmdd3/data/") + + +@pytest.fixture +def generate_MalaCards_ftp(): + return MalaCards() + + +def test_import_DisGeNet(generate_DisGeNet_ftp): + """ + Args: + generate_DisGeNet_ftp: + """ + assert generate_DisGeNet_ftp.data_path == "https://www.disgenet.org/static/disgenet_ap1/files/downloads/" + assert not generate_DisGeNet_ftp.get_disease_assocs(index="gene_name").empty + + +def test_annotate_DisGeNet(generate_TCGA_LUAD, generate_DisGeNet_ftp): + """ + Args: + generate_TCGA_LUAD: + generate_DisGeNet_ftp: + """ + generate_TCGA_LUAD.MessengerRNA.annotate_diseases(generate_DisGeNet_ftp, on="gene_name", ) + assert {'disease_associations'}.issubset(generate_TCGA_LUAD.MessengerRNA.annotations.columns) + + +def test_import_HMDD(generate_HMDD_ftp): + """ + Args: + generate_HMDD_ftp: + """ + assert generate_HMDD_ftp.data_path == "http://www.cuilab.cn/static/hmdd3/data/" + assert not generate_HMDD_ftp.get_disease_assocs(index="gene_name").empty + + +def test_annotate_HMDD(generate_TCGA_LUAD, generate_HMDD_ftp): + """ + Args: + generate_TCGA_LUAD: + generate_HMDD_ftp: + """ + generate_TCGA_LUAD.MicroRNA.annotate_diseases(generate_HMDD_ftp, on="gene_name", ) + assert {'disease_associations'}.issubset(generate_TCGA_LUAD.MicroRNA.annotations.columns) + + +def test_LncRNADisease(generate_LncRNADisease_ftp): + """ + Args: + generate_LncRNADisease_ftp: + """ + assert generate_LncRNADisease_ftp.data_path == "http://www.cuilab.cn/files/images/ldd/" + assert not generate_LncRNADisease_ftp.get_disease_assocs(index="gene_name").empty + + +def test_annotate_LncRNADisease(generate_TCGA_LUAD, generate_LncRNADisease_ftp): + """ + Args: + generate_TCGA_LUAD: + generate_LncRNADisease_ftp: + """ + generate_TCGA_LUAD.LncRNA.annotate_diseases(generate_LncRNADisease_ftp, on="gene_name", ) + assert {'disease_associations'}.issubset(generate_TCGA_LUAD.LncRNA.annotations.columns) + + +def test_import_MalaCards(generate_MalaCards_ftp): + """ + Args: + generate_MalaCards_ftp: + """ + assert generate_MalaCards_ftp.data_path == "http://zdzlab.einstein.yu.edu/1/hedd/"