"""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,
SPARQL_CONF,
)
from gn3.db.rdf.wiki import (
__sanitize_result,
get_wiki_entries_by_symbol,
get_comment_history,
update_wiki_comment,
)
GRAPH = "<http://cd-test.genenetwork.org>"
@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 = SPARQL_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 = SPARQL_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 = SPARQL_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",
})
