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authorMunyoki Kilyungi2024-09-23 12:27:38 +0300
committerBonfaceKilz2024-09-23 12:32:51 +0300
commitf10212c6423fa00b5209d617172a508c181547c2 (patch)
tree8372623c6cd1f2b9f57c9e5b225ebaf58b6f5719 /tests
parent05735bad5a38f47b6e30b05dc4fc754de3fbcbd6 (diff)
downloadgenenetwork3-f10212c6423fa00b5209d617172a508c181547c2.tar.gz
Fix or ignore pylint errors.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'tests')
-rw-r--r--tests/fixtures/rdf.py2
-rw-r--r--tests/unit/db/rdf/test_wiki.py45
2 files changed, 36 insertions, 11 deletions
diff --git a/tests/fixtures/rdf.py b/tests/fixtures/rdf.py
index 776a5d4..6d5b6aa 100644
--- a/tests/fixtures/rdf.py
+++ b/tests/fixtures/rdf.py
@@ -1,7 +1,7 @@
"""Test fixtures to set up a test named graph for loading RDF data."""
+import os
from requests.auth import HTTPDigestAuth
from flask import config
-import os
import requests
import pytest
diff --git a/tests/unit/db/rdf/test_wiki.py b/tests/unit/db/rdf/test_wiki.py
index 73ac2ef..5f36034 100644
--- a/tests/unit/db/rdf/test_wiki.py
+++ b/tests/unit/db/rdf/test_wiki.py
@@ -1,8 +1,26 @@
-"""Tests for gn3/db/rdf/wiki.py"""
+"""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
-from tests.fixtures.rdf import rdf_setup, get_sparql_auth_conf
import pytest
-import os
+
+# pylint: disable=W0611
+from tests.fixtures.rdf import (
+ rdf_setup,
+ get_sparql_auth_conf
+)
from gn3.db.rdf.wiki import (
__sanitize_result,
@@ -169,7 +187,7 @@ def test_sanitize_result(result, expected):
@pytest.mark.rdf
-def test_get_wiki_entries_by_symbol(rdf_setup):
+def test_get_wiki_entries_by_symbol(rdf_setup): # pylint: disable=W0613,W0621
"""Test that wiki entries are fetched correctly by symbol"""
result = get_wiki_entries_by_symbol(
symbol="ckb",
@@ -222,7 +240,10 @@ def test_get_wiki_entries_by_symbol(rdf_setup):
"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).",
+ "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,
@@ -240,7 +261,8 @@ def test_get_wiki_entries_by_symbol(rdf_setup):
@pytest.mark.rdf
-def test_get_comment_history(rdf_setup):
+def test_get_comment_history(rdf_setup): # pylint: disable=W0613,W0621
+ """Test fetching a comment's history from RDF"""
result = get_comment_history(
comment_id=1158,
sparql_uri=SPARQL_CONF["sparql_endpoint"],
@@ -277,7 +299,8 @@ def test_get_comment_history(rdf_setup):
"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.",
+ "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",
@@ -311,7 +334,9 @@ def test_get_comment_history(rdf_setup):
"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.",
+ "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",
@@ -328,9 +353,9 @@ def test_get_comment_history(rdf_setup):
@pytest.mark.rdf
-def test_update_wiki_comment(rdf_setup):
+def test_update_wiki_comment(rdf_setup): # pylint: disable=W0613,W0621
"""Test that a comment is updated correctly"""
- response = update_wiki_comment(
+ update_wiki_comment(
insert_dict={
"Id": 230,
"symbol": "Shh",