From 0d82533600cb5235f0fd0bc333ed555009efdf85 Mon Sep 17 00:00:00 2001 From: Cunliang Geng Date: Fri, 14 Jun 2024 10:34:08 +0200 Subject: [PATCH] Update test_nplinker_local.py --- tests/integration/test_nplinker_local.py | 36 ++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/tests/integration/test_nplinker_local.py b/tests/integration/test_nplinker_local.py index 55ce5a84..54144dd1 100644 --- a/tests/integration/test_nplinker_local.py +++ b/tests/integration/test_nplinker_local.py @@ -1,5 +1,9 @@ import os +import pickle import pytest +from nplinker.genomics import GCF +from nplinker.metabolomics import MolecularFamily +from nplinker.metabolomics import Spectrum from nplinker.nplinker import NPLinker from . import DATA_DIR @@ -70,3 +74,35 @@ def test_get_links(npl): for _, _, scores in lg.links: score = scores[scoring_method] assert score.value >= 0 + + +def test_save_data(npl): + scoring_method = "metcalf" + links = npl.get_links(npl.gcfs[:3], scoring_method) + + pickle_file = os.path.join(npl.output_dir, "npl.pkl") + npl.save_data(pickle_file, links) + + with open(pickle_file, "rb") as f: + bgcs, gcfs, spectra, mfs, strains, lg = pickle.load(f) + + # tests from `test_load_data` + assert len(bgcs) == 390 + assert len(gcfs) == 64 + assert len(spectra) == 24652 + assert len(mfs) == 29 + assert len(strains) == 46 + + # tests from `test_get_links` + for obj1, obj2, scores in lg.links: + score = scores[scoring_method] + assert score.value >= 0 + + if isinstance(obj1, GCF): + assert obj1 in gcfs + elif isinstance(obj1, Spectrum): + assert obj1 in spectra + elif isinstance(obj1, MolecularFamily): + assert obj1 in mfs + else: + assert False