diff options
Diffstat (limited to 'tests/unit/db/rdf')
| -rw-r--r-- | tests/unit/db/rdf/data.py | 199 | ||||
| -rw-r--r-- | tests/unit/db/rdf/test_wiki.py | 50 |
2 files changed, 249 insertions, 0 deletions
diff --git a/tests/unit/db/rdf/data.py b/tests/unit/db/rdf/data.py new file mode 100644 index 0000000..6bc612f --- /dev/null +++ b/tests/unit/db/rdf/data.py @@ -0,0 +1,199 @@ +"""Some test data to be used in RDF data.""" + +LPL_RIF_ENTRIES = { + "@context": { + "dct": "http://purl.org/dc/terms/", + "gnt": "http://genenetwork.org/term/", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "symbol": "gnt:symbol", + "species": "gnt:species", + "taxonomic_id": "skos:notation", + "gene_id": "gnt:hasGeneId", + "pubmed_id": "dct:references", + "created": "dct:created", + "comment": "rdfs:comment", + "version": "dct:hasVersion", + }, + "data": [ + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-02-23 20:40:00", + "pubmed_id": 36763533, + "comment": "Angiopoietin-like protein 4/8 complex-mediated plasmin generation \ +leads to cleavage of the complex and restoration of LPL activity.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-04-07 20:39:00", + "pubmed_id": 36652113, + "comment": "The breast cancer microenvironment and lipoprotein lipase: \ +Another negative notch for a beneficial enzyme?", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-04-27 20:33:00", + "pubmed_id": 36519761, + "comment": "Parkin regulates neuronal lipid homeostasis through \ +SREBP2-lipoprotein lipase pathway-implications for Parkinson's disease.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-05-22 20:32:00", + "pubmed_id": 36708756, + "comment": "Plasma Lipoprotein Lipase Is Associated with Risk of \ +Future Major Adverse Cardiovascular Events in Patients Following Carotid Endarterectomy.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-07-04 21:12:00", + "pubmed_id": 37155355, + "comment": "Inverse association between apolipoprotein C-II and \ +cardiovascular mortality: role of lipoprotein lipase activity modulation.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-07-13 20:35:00", + "pubmed_id": 37432202, + "comment": "Effect of the Interaction between Seaweed Intake and LPL \ +Polymorphisms on Metabolic Syndrome in Middle-Aged Korean Adults.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-08-14 20:37:00", + "pubmed_id": 37568214, + "comment": "Frameshift coding sequence variants in the LPL gene: identification \ +of two novel events and exploration of the genotype-phenotype relationship for \ +variants reported to date.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-08-22 20:29:00", + "pubmed_id": 37550668, + "comment": "The East Asian-specific LPL p.Ala288Thr (c.862G > A) missense \ +variant exerts a mild effect on protein function.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-09-12 20:35:00", + "pubmed_id": 37128695, + "comment": "Interaction between APOE, APOA1, and LPL Gene Polymorphisms \ +and Variability in Changes in Lipid and Blood Pressure following Orange Juice Intake: \ +A Pilot Study.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-09-25 09:33:00", + "pubmed_id": 37427758, + "comment": "Variants within the LPL gene confer susceptility to \ +diabetic kidney disease and rapid decline in kidney function in Chinese patients \ +with type 2 diabetes.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-11-01 08:55:00", + "pubmed_id": 37901192, + "comment": "The Association of Adipokines and Myokines in the \ +Blood of Obese Children and Adolescents with Lipoprotein Lipase rs328 Gene Variants.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-11-10 08:44:00", + "pubmed_id": 37871217, + "comment": "The lipoprotein lipase that is shuttled into \ +capillaries by GPIHBP1 enters the glycocalyx where it mediates lipoprotein processing.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-12-28 20:33:00", + "pubmed_id": 37858495, + "comment": "Clinical profile, genetic spectrum and therapy \ +evaluation of 19 Chinese pediatric patients with lipoprotein lipase deficiency.", + "taxonomic_id": 9606, + }, + { + "gene_id": 4023, + "version": 5, + "species": "Homo sapiens", + "symbol": "LPL", + "created": "2023-12-29 20:33:00", + "pubmed_id": 38114521, + "comment": "Developing a model to predict the early risk of \ +hypertriglyceridemia based on inhibiting lipoprotein lipase (LPL): a translational study.", + "taxonomic_id": 9606, + }, + { + "gene_id": 16956, + "version": 5, + "species": "Mus musculus", + "symbol": "Lpl", + "created": "2023-04-27 20:33:00", + "pubmed_id": 36519761, + "comment": "Parkin regulates neuronal lipid homeostasis through \ +SREBP2-lipoprotein lipase pathway-implications for Parkinson's disease.", + "taxonomic_id": 10090, + }, + { + "gene_id": 24539, + "version": 5, + "species": "Rattus norvegicus", + "symbol": "Lpl", + "created": "2023-12-29 20:33:00", + "pubmed_id": 38114521, + "comment": "Developing a model to predict the early risk of \ +hypertriglyceridemia based on inhibiting lipoprotein lipase (LPL): a translational study.", + "taxonomic_id": 10116, + }, + ], +} diff --git a/tests/unit/db/rdf/test_wiki.py b/tests/unit/db/rdf/test_wiki.py index 3abf3ad..bab37ce 100644 --- a/tests/unit/db/rdf/test_wiki.py +++ b/tests/unit/db/rdf/test_wiki.py @@ -22,11 +22,15 @@ from tests.fixtures.rdf import ( SPARQL_CONF, ) +from tests.unit.db.rdf.data import LPL_RIF_ENTRIES + from gn3.db.rdf.wiki import ( __sanitize_result, get_wiki_entries_by_symbol, get_comment_history, update_wiki_comment, + get_rif_entries_by_symbol, + delete_wiki_entries_by_id, ) GRAPH = "<http://cd-test.genenetwork.org>" @@ -396,3 +400,49 @@ def test_update_wiki_comment(rdf_setup): # pylint: disable=W0613,W0621 "version": 3, "web_url": "http://some-website.com", }) + + +@pytest.mark.rdf +def test_get_rif_entries_by_symbol(rdf_setup): # pylint: disable=W0613,W0621 + """Test fetching NCBI Rif Metadata from RDF""" + sparql_conf = SPARQL_CONF + entries = get_rif_entries_by_symbol( + symbol="Lpl", + sparql_uri=sparql_conf["sparql_endpoint"], + graph=GRAPH, + ) + assert len(LPL_RIF_ENTRIES["data"]) == len(entries["data"]) + for result, expected in zip(LPL_RIF_ENTRIES["data"], entries["data"]): + TestCase().assertDictEqual(result, expected) + + +@pytest.mark.rdf +def test_delete_wiki_entries_by_id(rdf_setup): # pylint: disable=W0613,W0621 + """Test deleting a given RIF Wiki entry""" + sparql_conf = SPARQL_CONF + delete_wiki_entries_by_id( + 230, + sparql_user=sparql_conf["sparql_user"], + sparql_password=sparql_conf["sparql_password"], + sparql_auth_uri=sparql_conf["sparql_auth_uri"], + graph=GRAPH) + entries = get_comment_history( + comment_id=230, + sparql_uri=sparql_conf["sparql_endpoint"], + graph=GRAPH, + ) + assert len(entries["data"]) == 0 + + # Deleting a non-existent entry has no effect + delete_wiki_entries_by_id( + 199999, + sparql_user=sparql_conf["sparql_user"], + sparql_password=sparql_conf["sparql_password"], + sparql_auth_uri=sparql_conf["sparql_auth_uri"], + graph=GRAPH) + entries = get_comment_history( + comment_id=230, + sparql_uri=sparql_conf["sparql_endpoint"], + graph=GRAPH, + ) + assert len(entries["data"]) == 0 |