Add RDF test cases.

* pytest.ini: Add rdf pytest marker.
* tests/test_data/ttl-files/test-data.ttl: New file with turtle test
data for RIF editing.
* tests/unit/db/rdf/test_wiki.py (test_sanitize_result): New test
case.
(test_get_comment_history): Ditto.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 216 insertions, 1 deletions

diff --git a/tests/unit/db/rdf/test_wiki.py b/tests/unit/db/rdf/test_wiki.py
index e8f0e62..99ecab0 100644
--- a/tests/unit/db/rdf/test_wiki.py
+++ b/tests/unit/db/rdf/test_wiki.py
@@ -1,8 +1,18 @@
 """Tests for gn3/db/rdf/wiki.py"""
+from unittest import TestCase
 
 import pytest
+import os
 
-from gn3.db.rdf.wiki import __sanitize_result
+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
@@ -155,3 +165,208 @@ from gn3.db.rdf.wiki import __sanitize_result
 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():
+    """Test that wiki entries are fetched correctly by symbol"""
+    result = get_wiki_entries_by_symbol(
+        symbol="ckb",
+        sparql_uri=os.environ.get("SPARQL_ENDPOINT", "http://localhost:9082/sparql"),
+        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():
+    result = get_comment_history(
+        comment_id=1158,
+        sparql_uri=os.environ.get("SPARQL_ENDPOINT", "http://localhost:9082/sparql"),
+        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": "",
+            },
+        ],
+    }
+    # breakpoint()
+    TestCase().assertDictEqual(result, expected)
+
+
+@pytest.mark.rdf
+def test_update_wiki_comment(rdf_setup):
+    """Test that a comment is updated correctly"""
+    response = 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",
+    })