def setUpClass(cls) -> None:
json_metrics = getMetrics()
factory = FAIRMetricsFactory()
# for i in range(1,3):
try:
# metrics.append(factory.get_metric("test_f1"))
# metrics.append(factory.get_metric("test_r2"))
for metric in json_metrics:
# remove "FAIR Metrics Gen2" from metric name
name = metric["name"].replace("FAIR Metrics Gen2- ", "")
# same but other syntax because of typo
name = name.replace("FAIR Metrics Gen2 - ", "")
principle = metric["principle"].rsplit("/", 1)[-1]
cls.metrics.append(
factory.get_metric(
name,
metric["@id"],
metric["description"],
metric["smarturl"],
principle,
metric["creator"],
metric["created_at"],
metric["updated_at"],
)
)
except ValueError as e:
print(f"no metrics implemention for {e}")
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_R13_workflowhub(self):
wf = ReuseTestCase.wf
res = FAIRMetricsFactory.get_R13(
web_resource=wf, impl=Implem.FAIR_CHECKER
).evaluate()
logging.info(res)
self.assertEqual(res.get_score(), str(Result.WEAK.value))
def test_R13_biotools(self):
biotools = ReuseTestCase.tool
res = FAIRMetricsFactory.get_R13(
web_resource=biotools, impl=Implem.FAIR_CHECKER
).evaluate()
logging.info(res)
self.assertEqual(res.get_score(), str(Result.WEAK.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_R11_biotools(self):
biotools = ReuseTestCase.tool
res = FAIRMetricsFactory.get_R11(
web_resource=biotools, impl=Implem.FAIR_CHECKER
).evaluate()
logging.info(res)
self.assertEqual(
res.get_score(), str(Result.NO.value)
) # TODO to be fixed with Thomas use the Result enum rather than int values
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 test_cached_F2B_biotools(self):
biotools = FindabilityTestCase.tool
res4 = FAIRMetricsFactory.get_R11(web_resource=biotools,
impl=Implem.FAIR_CHECKER).evaluate()
logging.info(res4)
self.assertEqual(res4.get_score(), str(Result.NO.value))
res1 = FAIRMetricsFactory.get_F2B(web_resource=biotools,
impl=Implem.FAIR_CHECKER).evaluate()
logging.info(res1)
self.assertEqual(res1.get_score(), str(Result.WEAK.value))
res2 = FAIRMetricsFactory.get_F2B(web_resource=biotools,
impl=Implem.FAIR_CHECKER).evaluate()
logging.info(res2)
self.assertEqual(res2.get_score(), str(Result.WEAK.value))
res3 = FAIRMetricsFactory.get_I2(web_resource=biotools,
impl=Implem.FAIR_CHECKER).evaluate()
logging.info(res3)
self.assertEqual(res3.get_score(), str(Result.WEAK.value))
def eval_metrics(web_res):
metrics_collection = []
# metrics_collection.append(FAIRMetricsFactory.get_F1A(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_I2(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
return row, row_time
def test_F2A_biotools(self):
biotools = FindabilityTestCase.tool
res = FAIRMetricsFactory.get_F2A(web_resource=biotools,
impl=Implem.FAIR_CHECKER).evaluate()
logging.info(res)
self.assertEqual(res.get_score(), str(Result.STRONG.value))
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_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 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))