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fix tox
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@YojanaGadiya
YojanaGadiya committed Oct 11, 2024
1 parent 365ee3d commit 346b568
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Showing 2 changed files with 15 additions and 13 deletions.
4 changes: 2 additions & 2 deletions src/pyBiodatafuse/graph/generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
import os
import pickle
from logging import Logger
from typing import Any
from typing import Any, Dict

import networkx as nx
import pandas as pd
Expand Down Expand Up @@ -921,7 +921,7 @@ def build_networkx_graph(

def save_graph(
combined_df: pd.DataFrame,
combined_metadata: dict[Any, Any],
combined_metadata: Dict[Any, Any],
disease_compound: pd.DataFrame = None,
graph_name: str = "combined",
graph_dir: str = "examples/usecases/",
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24 changes: 13 additions & 11 deletions tests/annotators/test_disgenet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,9 @@
from unittest.mock import Mock, patch

import pandas as pd
from requests import Session
from requests import Response, Session

from pyBiodatafuse.annotators import disgenet
from pyBiodatafuse.annotators.disgenet import get_gene_disease, get_version_disgenet
from pyBiodatafuse.constants import DISGENET_DISEASE_COL

data_file_folder = os.path.join(os.path.dirname(__file__), "data")
Expand All @@ -22,14 +21,18 @@ class TestDisgenet(unittest.TestCase):
"""Test the DISGENET class."""

@patch.object(Session, "get")
def test_get_version_disgenet(self, mock_sparql_version):
"""Test that the API endpoint returns the expected get_version_bgee results."""
mock_sparql_version.side_effect = {
def test_get_version_disgenet(self, requests_get):
"""Test that the API endpoint returns the expected get_version_disgenet results."""
successful_response = Mock(Response)
successful_response.status_code = 406
successful_response.json.return_value = {
"status": "OK",
"payload": {"lastUpdate": "10 Jul 2024", "version": "DISGENET v24.2"},
"httpStatus": 200,
}
requests_get.return_value = successful_response

obtained_version = get_version_disgenet(api_key="test")
obtained_version = disgenet.get_version_disgenet(api_key="test")

expected_version = {"lastUpdate": "10 Jul 2024", "version": "DISGENET v24.2"}

Expand All @@ -39,10 +42,7 @@ def test_get_version_disgenet(self, mock_sparql_version):
def test_get_gene_disease(self, mock_post_gene_disease):
"""Test the get_gene_disease function."""
disgenet.get_version_disgenet = Mock(
return_value={
"status": "OK",
"payload": {"lastUpdate": "10 Jul 2024", "version": "DISGENET v24.2"},
}
return_value={"lastUpdate": "10 Jul 2024", "version": "DISGENET v24.2"}
) # Mock the version call
disgenet.check_endpoint_disgenet = Mock(return_value=True)

Expand All @@ -58,7 +58,9 @@ def test_get_gene_disease(self, mock_post_gene_disease):
mock_post_gene_disease.return_value.ok = True
mock_post_gene_disease.return_value.text = '{"status":"OK","paging":{"pageSize":100,"totalElements":6,"totalElementsInPage":6,"currentPageNumber":0},"warnings":["gene_ensembl_id > The parameter value is empty / unspecified.","gene_symbol > The parameter value is empty / unspecified.","disease > The parameter value is empty / unspecified.","chemical > The parameter value is empty / unspecified.","dis_type > The parameter value is empty / unspecified.","dis_class_list > The parameter value is empty / unspecified.","min_score > The parameter value is unspecified or not a double number.","max_score > The parameter value is unspecified or not a double number.","min_ei > The parameter value is unspecified or not a double number.","max_ei > The parameter value is unspecified or not a double number.","min_dsi > The parameter value is unspecified or not a double number.","max_dsi > The parameter value is unspecified or not a double number.","min_dpi > The parameter value is unspecified or not a double number.","max_dpi > The parameter value is unspecified or not a double number.","min_pli > The parameter value is unspecified or not a double number.","max_pli > The parameter value is unspecified or not a double number."],"requestpar":{"gene_ncbi_id":"199857","source":"CURATED","page_number":0},"userinfo":{"profile":"ACADEMIC","profileDescription":"Your DISGENET profile is ACADEMIC; you can access DISGENET REST endpoints with restrictions."},"payload":[{"assocID":15912171,"symbolOfGene":"ALG14","geneNcbiID":199857,"geneEnsemblIDs":["ENSG00000172339"],"geneNcbiType":"protein-coding","geneDSI":0.622,"geneDPI":0.542,"genepLI":6.9786E-5,"geneProteinStrIDs":["Q96F25"],"geneProteinClassIDs":[],"geneProteinClassNames":[],"diseaseVocabularies":["MESH_D018981","NCI_C84615","ORDO_137","DO_5212","MONDO_0015286","UMLS_C0282577"],"diseaseName":"Congenital Disorders of Glycosylation","diseaseType":"disease","diseaseUMLSCUI":"C0282577","diseaseClasses_MSH":["Congenital, Hereditary, and Neonatal Diseases and Abnormalities (C16)","Nutritional and Metabolic Diseases (C18)"],"diseaseClasses_UMLS_ST":["Disease or Syndrome (T047)"],"diseaseClasses_DO":["physical disorder (0080015)","genetic disease (630)","disease of metabolism (0014667)"],"diseaseClasses_HPO":[],"chemicalsIncludedInEvidence":null,"numberPmidsWithChemsIncludedInEvidenceBySource":[],"score":0.6000000000000001,"yearInitial":2005,"yearFinal":2022,"el":"Limited","ei":1.0},{"assocID":20783606,"symbolOfGene":"ALG14","geneNcbiID":199857,"geneEnsemblIDs":["ENSG00000172339"],"geneNcbiType":"protein-coding","geneDSI":0.622,"geneDPI":0.542,"genepLI":6.9786E-5,"geneProteinStrIDs":["Q96F25"],"geneProteinClassIDs":[],"geneProteinClassNames":[],"diseaseVocabularies":["MESH_D020294","NCI_C84647","ORDO_590","DO_3635","MONDO_0018940","UMLS_C0751882"],"diseaseName":"Myasthenic Syndromes, Congenital","diseaseType":"disease","diseaseUMLSCUI":"C0751882","diseaseClasses_MSH":["Congenital, Hereditary, and Neonatal Diseases and Abnormalities (C16)","Nervous System Diseases (C10)"],"diseaseClasses_UMLS_ST":["Disease or Syndrome (T047)"],"diseaseClasses_DO":["physical disorder (0080015)","disease of anatomical entity (7)"],"diseaseClasses_HPO":[],"chemicalsIncludedInEvidence":null,"numberPmidsWithChemsIncludedInEvidenceBySource":[],"score":0.6000000000000001,"yearInitial":null,"yearFinal":null,"el":null,"ei":1.0},{"assocID":25777482,"symbolOfGene":"ALG14","geneNcbiID":199857,"geneEnsemblIDs":["ENSG00000172339"],"geneNcbiType":"protein-coding","geneDSI":0.622,"geneDPI":0.542,"genepLI":6.9786E-5,"geneProteinStrIDs":["Q96F25"],"geneProteinClassIDs":[],"geneProteinClassNames":[],"diseaseVocabularies":["OMIM_612866","OMIM_616227","DO_0110658","MONDO_0014542","UMLS_C4015596"],"diseaseName":"MYASTHENIC SYNDROME, CONGENITAL, 15","diseaseType":"disease","diseaseUMLSCUI":"C4015596","diseaseClasses_MSH":[],"diseaseClasses_UMLS_ST":["Disease or Syndrome (T047)"],"diseaseClasses_DO":["genetic disease (630)","physical disorder (0080015)","disease of anatomical entity (7)"],"diseaseClasses_HPO":[],"chemicalsIncludedInEvidence":null,"numberPmidsWithChemsIncludedInEvidenceBySource":[],"score":0.6,"yearInitial":2013,"yearFinal":2021,"el":null,"ei":1.0},{"assocID":26279064,"symbolOfGene":"ALG14","geneNcbiID":199857,"geneEnsemblIDs":["ENSG00000172339"],"geneNcbiType":"protein-coding","geneDSI":0.622,"geneDPI":0.542,"genepLI":6.9786E-5,"geneProteinStrIDs":["Q96F25"],"geneProteinClassIDs":[],"geneProteinClassNames":[],"diseaseVocabularies":["OMIM_612866","OMIM_619036","MONDO_0033619","UMLS_C5436652"],"diseaseName":"MYOPATHY, EPILEPSY, AND PROGRESSIVE CEREBRAL ATROPHY","diseaseType":"disease","diseaseUMLSCUI":"C5436652","diseaseClasses_MSH":[],"diseaseClasses_UMLS_ST":["Disease or Syndrome (T047)"],"diseaseClasses_DO":[],"diseaseClasses_HPO":[],"chemicalsIncludedInEvidence":null,"numberPmidsWithChemsIncludedInEvidenceBySource":[],"score":0.5,"yearInitial":2017,"yearFinal":2017,"el":null,"ei":1.0},{"assocID":26354111,"symbolOfGene":"ALG14","geneNcbiID":199857,"geneEnsemblIDs":["ENSG00000172339"],"geneNcbiType":"protein-coding","geneDSI":0.622,"geneDPI":0.542,"genepLI":6.9786E-5,"geneProteinStrIDs":["Q96F25"],"geneProteinClassIDs":[],"geneProteinClassNames":[],"diseaseVocabularies":["ORDO_353327","EFO_0700079","UMLS_C5680989"],"diseaseName":"Congenital myasthenic syndromes with glycosylation defect","diseaseType":"disease","diseaseUMLSCUI":"C5680989","diseaseClasses_MSH":["Congenital, Hereditary, and Neonatal Diseases and Abnormalities (C16)","Nervous System Diseases (C10)"],"diseaseClasses_UMLS_ST":["Disease or Syndrome (T047)"],"diseaseClasses_DO":[],"diseaseClasses_HPO":[],"chemicalsIncludedInEvidence":null,"numberPmidsWithChemsIncludedInEvidenceBySource":[],"score":0.4,"yearInitial":2013,"yearFinal":2013,"el":null,"ei":1.0},{"assocID":26279043,"symbolOfGene":"ALG14","geneNcbiID":199857,"geneEnsemblIDs":["ENSG00000172339"],"geneNcbiType":"protein-coding","geneDSI":0.622,"geneDPI":0.542,"genepLI":6.9786E-5,"geneProteinStrIDs":["Q96F25"],"geneProteinClassIDs":[],"geneProteinClassNames":[],"diseaseVocabularies":["OMIM_612866","OMIM_619031","MONDO_0033572","UMLS_C5436646"],"diseaseName":"INTELLECTUAL DEVELOPMENTAL DISORDER WITH EPILEPSY, BEHAVIORAL ABNORMALITIES, AND COARSE FACIES","diseaseType":"disease","diseaseUMLSCUI":"C5436646","diseaseClasses_MSH":[],"diseaseClasses_UMLS_ST":["Disease or Syndrome (T047)"],"diseaseClasses_DO":[],"diseaseClasses_HPO":[],"chemicalsIncludedInEvidence":null,"numberPmidsWithChemsIncludedInEvidenceBySource":[],"score":0.4,"yearInitial":2018,"yearFinal":2018,"el":null,"ei":1.0}]}'

obtained_data, metadata = get_gene_disease(api_key="test", bridgedb_df=bridgedb_dataframe)
obtained_data, metadata = disgenet.get_gene_disease(
api_key="test", bridgedb_df=bridgedb_dataframe
)

expected_data = pd.Series(
[
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