"""Tests for gn3/db/rdf/wiki.py NOTE: Some errors like W0611, W0613, and W0621 are due to Pytest's usage of fixtures. This errors are Ignored for now. The alternative would be to install pylint-pytest: https://github.com/pylint-dev/pylint-pytest More discussions: https://github.com/PyCQA/meta/issues/56 """ from unittest import TestCase import pytest # pylint: disable=W0611 from tests.fixtures.rdf import ( rdf_setup, get_sparql_auth_conf ) from gn3.db.rdf.wiki import ( __sanitize_result, get_wiki_entries_by_symbol, get_comment_history, update_wiki_comment, ) GRAPH = "" @pytest.mark.unit_test @pytest.mark.parametrize( ("result", "expected"), ( ( { "categories": "", "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": "", "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, { "categories": [], "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": [], "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, ), ( { "categories": "some-category", "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": "", "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, { "categories": ["some-category"], "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": [], "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, ), ( { "categories": "", "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": "21", "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, { "categories": [], "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": [21], "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, ), ( { "categories": "", "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": 21, "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, { "categories": [], "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": [21], "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, ), ( { "categories": "", "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": [21, 22], "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, { "categories": [], "comment": "comment", "created": "2006-12-23 17:19:14", "email": "XXX@XXX.edu", "initial": "KMz", "pubmed_ids": [21, 22], "reason": "add", "species": "mouse", "symbol": "Sfrs3", "version": 0, "web_url": "", }, ), ({}, {}), ), ) def test_sanitize_result(result, expected): """Test that the JSON-LD result is sanitized correctly""" assert __sanitize_result(result) == expected @pytest.mark.rdf def test_get_wiki_entries_by_symbol(rdf_setup): # pylint: disable=W0613,W0621 """Test that wiki entries are fetched correctly by symbol""" sparql_conf = get_sparql_auth_conf() result = get_wiki_entries_by_symbol( symbol="ckb", sparql_uri=sparql_conf["sparql_endpoint"], graph=GRAPH, ) expected = { "@context": { "categories": "gnt:belongsToCategory", "comment": "rdfs:comment", "created": "dct:created", "data": "@graph", "dct": "http://purl.org/dc/terms/", "email": "foaf:mbox", "foaf": "http://xmlns.com/foaf/0.1/", "gn": "http://genenetwork.org/id/", "gnc": "http://genenetwork.org/category/", "gnt": "http://genenetwork.org/term/", "id": "dct:identifier", "initial": "gnt:initial", "pubmed_ids": "dct:references", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#>", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "reason": "gnt:reason", "species": "gnt:species", "symbol": "rdfs:label", "type": "@type", "version": "gnt:hasVersion", "web_url": "foaf:homepage", }, "data": [ { "@id": "gn:wiki-1106-0", "categories": [], "comment": "high similarities on four locations on three different chromosomes", "created": "2007-01-16 10:06:34", "email": "XXX@XXX.com", "id": 1106, "initial": "dcc", "pubmed_ids": [], "reason": "", "species": "mouse", "symbol": "Ckb", "version": 0, "web_url": "", }, { "@id": "gn:wiki-5006-0", "categories": [ "Genetic variation and alleles", "Interactions: mRNA, proteins, other molecules", ], "comment": "Strong cis eQTL in brain RNA-seq data \ (LRS of 29 high B allele). Highly expressed in almost all neurons \ (not just interneurons). Trans targets of CKB include striatin (STRN) \ and C1QL3 (CTRP13).", "created": "2012-11-11 10:37:11", "email": "XXX@XXX.com", "id": 5006, "initial": "", "pubmed_ids": [], "reason": "", "species": "mouse", "symbol": "Ckb", "version": 0, "web_url": "", }, ], } TestCase().assertDictEqual(result, expected) @pytest.mark.rdf def test_get_comment_history(rdf_setup): # pylint: disable=W0613,W0621 """Test fetching a comment's history from RDF""" sparql_conf = get_sparql_auth_conf() result = get_comment_history( comment_id=1158, sparql_uri=sparql_conf["sparql_endpoint"], graph=GRAPH, ) expected = { "@context": { "categories": "gnt:belongsToCategory", "comment": "rdfs:comment", "created": "dct:created", "data": "@graph", "dct": "http://purl.org/dc/terms/", "email": "foaf:mbox", "foaf": "http://xmlns.com/foaf/0.1/", "gn": "http://genenetwork.org/id/", "gnc": "http://genenetwork.org/category/", "gnt": "http://genenetwork.org/term/", "id": "dct:identifier", "initial": "gnt:initial", "pubmed_ids": "dct:references", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#>", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "reason": "gnt:reason", "species": "gnt:species", "symbol": "rdfs:label", "type": "@type", "version": "gnt:hasVersion", "web_url": "foaf:homepage", }, "data": [ { "@id": "gn:wiki-1158-2", "categories": [ "Probes and probe sets", "Transcriptional and translation control", ], "comment": "Validated strong cis-QTL in CNS using allele-specific \ expression (ASE) SNaPshot assay. Possible 3' UTR variants.", "created": "2007-04-05 09:11:05", "email": "XXX@XXX.com", "initial": "dcc", "pubmed_ids": [], "reason": "new data", "species": "mouse", "symbol": "Lpl", "version": 2, "web_url": "", }, { "@id": "gn:wiki-1158-1", "categories": [ "Probes and probe sets", "Transcriptional and translation control", ], "comment": "putative 3' UTR variants", "created": "2007-02-09 09:23:40", "email": "XXX@XXX.com", "initial": "dcc", "reason": "", "pubmed_ids": [], "species": "mouse", "symbol": "Lpl", "version": 1, "web_url": "", }, { "@id": "gn:wiki-1158-0", "categories": [ "Probes and probe sets", "Transcriptional and translation control", ], "comment": "Validated strong cis-QTL in CNS using allele-specific \ expression (ASE) SNaPshot assay (Daniel Ciobanu and al., 2007). \ Possible 3' UTR variants.", "created": "2007-05-08 14:46:07", "email": "XXX@XXX.com", "initial": "dcc", "pubmed_ids": [], "reason": "addition", "species": "mouse", "symbol": "Lpl", "version": 0, "web_url": "", }, ], } TestCase().assertDictEqual(result, expected) @pytest.mark.rdf def test_update_wiki_comment(rdf_setup): # pylint: disable=W0613,W0621 """Test that a comment is updated correctly""" sparql_conf = get_sparql_auth_conf() update_wiki_comment( insert_dict={ "Id": 230, "symbol": "Shh", "PubMed_ID": "2 3 4", "email": "test@test.com", "comment": "Updated comment", "createtime": "2007-01-16 11:06:34", "weburl": "http://some-website.com", "initial": "BMK", "reason": "Testing", "versionId": 3, "species": "mouse", "categories": [], }, sparql_user=sparql_conf["sparql_user"], sparql_password=sparql_conf["sparql_password"], sparql_auth_uri=sparql_conf["sparql_auth_uri"], graph=GRAPH, ) updated_history = get_comment_history( comment_id=230, sparql_uri=sparql_conf["sparql_endpoint"], graph=GRAPH, )["data"] assert len(updated_history) == 4 TestCase().assertDictEqual(updated_history[0], { "@id": "gn:wiki-230-3", "categories": [], "comment": "Updated comment", "created": "2007-01-16 11:06:34", "email": "test@test.com", "initial": "BMK", "pubmed_ids": [2, 3, 4], "reason": "Testing", "species": "mouse", "symbol": "Shh", "version": 3, "web_url": "http://some-website.com", })