def test_identifiers_dataverse(self):
dataverse = WebResource(
"https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/P27LDX"
)
res = FAIRMetricsFactory.get_F1B(web_resource=dataverse).evaluate()
print(res)
self.assertEqual(res.get_score(), str(Result.NO.value))
def test_F1A_biotools_none(self):
metric_f1a = FAIRMetricsFactory.get_F1A(impl=Implem.FAIR_CHECKER)
web_resource = WebResource("https://bio.tools/bwa")
metric_f1a.set_web_resource(web_resource)
print(metric_f1a)
res = metric_f1a.evaluate()
logging.info(res)
self.assertEqual(res.get_score(), str(Result.STRONG.value))
def test_F1A_dataverse(self):
dataverse = WebResource(
# "https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/P27LDX"
"https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/DOMEHB"
# "https://data.inrae.fr/api/datasets/export?exporter=schema.org&persistentId=doi%3A10.15454/DOMEHB"
)
res = FAIRMetricsFactory.get_F1A(web_resource=dataverse,
impl=Implem.FAIR_CHECKER).evaluate()
logging.info(res)
self.assertEqual(res.get_score(), str(Result.STRONG.value))
def mass_eval(samples):
evals = []
exec_time = []
for url, graph in tqdm(samples.items()):
wr = WebResource(url=url, rdf_graph=graph)
row, row_time = eval_metrics(wr)
evals.append(row)
exec_time.append(row_time)
return evals, exec_time
def test_EDAM(self):
EDAM_KG = ConjunctiveGraph()
# EDAM_KG.parse("https://edamontology.org/EDAM.owl")
EDAM_KG.parse(
"/Users/gaignard-a/Documents/Dev/edamverify/src/EDAM.owl")
print(f"Loaded {len(EDAM_KG)} triples.")
edam = WebResource(
"file:///Users/gaignard-a/Documents/Dev/edamverify/src/EDAM.owl",
rdf_graph=EDAM_KG,
)
print(len(edam.get_rdf()))
self.assertGreater(len(edam.get_rdf()), 36000)
web_res = edam
metrics_collection = []
metrics_collection.append(FAIRMetricsFactory.get_2(web_res))
metrics_collection.append(FAIRMetricsFactory.get_F1B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_F2A(web_res))
metrics_collection.append(FAIRMetricsFactory.get_F2B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I1(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I1A(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I1B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I2(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I2A(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I2B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I3(web_res))
metrics_collection.append(FAIRMetricsFactory.get_R11(web_res))
metrics_collection.append(FAIRMetricsFactory.get_R12(web_res))
metrics_collection.append(FAIRMetricsFactory.get_R13(web_res))
row = {"ID": web_res.get_url()}
row_time = {"ID": web_res.get_url()}
for m in metrics_collection:
ts1 = time.time()
e = m.evaluate()
duration = round((time.time() - ts1), 2)
if e is not None:
row[m.get_principle_tag()] = e.get_score()
row_time[m.get_principle_tag()] = duration
print(row)
def setUpClass(cls) -> None:
super().setUpClass()
cls.tool = WebResource(cls.uri_tool)
cls.wf = WebResource(cls.uri_wf)
def test_identifiers_datacite(self):
datacite = WebResource(
"https://search.datacite.org/works/10.7892/boris.108387")
res = FAIRMetricsFactory.get_F1B(web_resource=datacite).evaluate()
print(res)
self.assertEqual(res.get_score(), str(Result.NO.value))
def test_fairchecker(self):
bwa = WebResource("https://fair-checker.france-bioinformatique.fr/")
logging.info(f"{len(bwa.get_rdf())} loaded RDF triples")
def test_workflowhub(self):
bwa = WebResource("https://workflowhub.eu/workflows/263")
logging.info(f"{len(bwa.get_rdf())} loaded RDF triples")
self.assertGreaterEqual(len(bwa.get_rdf()), 28)
turtle = bwa.get_rdf().serialize(format="turtle")
self.assertTrue("sc:ComputationalWorkflow" in turtle)
def test_dataverse(self):
dataverse = WebResource(
"https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/P27LDX"
)
logging.info(f"{len(dataverse.get_rdf())} loaded RDF triples")
self.assertGreaterEqual(len(dataverse.get_rdf()), 9)
def test_biotools(self):
bwa = WebResource("http://bio.tools/bwa")
logging.info(f"{len(bwa.get_rdf())} loaded RDF triples")
self.assertGreaterEqual(len(bwa.get_rdf()), 124)
def test_I3_biotools(self):
biotools = WebResource("http://bio.tools/bwa")
res = FAIRMetricsFactory.get_I3(web_resource=biotools,
impl=Implem.FAIR_CHECKER).evaluate()
logging.info(res)
self.assertEqual(res.get_score(), str(Result.STRONG.value))