Pass in insert_dict instead of payload in "get_wiki_entries".

* gn3/api/metadata_api/wiki.py (edit_wiki) [insert_dict]: Add species,
categories fields.
[update_wiki_comment]: Pass in insert_dict, and get rid of redundant
keys.  Directly pass in sparql_auth's conf params instead of a dict.
* gn3/db/rdf/wiki.py (get_next_comment_version): Get rid of redundant
params.  Use fields directly from insert_dict.  Directly pass in
sparql_auth's conf params instead of a dict.

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

2 files changed, 34 insertions, 39 deletions

diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py
index 8aa0b37..70045aa 100644
--- a/gn3/api/metadata_api/wiki.py
+++ b/gn3/api/metadata_api/wiki.py
@@ -25,20 +25,21 @@ def edit_wiki(comment_id: int):
     # FIXME: attempt to check and fix for types here with relevant errors
     payload: Dict[str, Any] = request.json  # type: ignore
     pubmed_ids = [str(x) for x in payload.get("pubmed_ids", [])]
-    created = datetime.datetime.now(datetime.timezone.utc).strftime(
-        "%Y-%m-%d %H:%M:%S"
-    )
     insert_dict = {
         "Id": comment_id,
         "symbol": payload["symbol"],
         "PubMed_ID": " ".join(pubmed_ids),
         "comment": payload["comment"],
         "email": payload["email"],
-        "createtime": created,
+        "createtime": datetime.datetime.now(datetime.timezone.utc).strftime(
+            "%Y-%m-%d %H:%M:%S"
+        ),
         "user_ip": request.environ.get("HTTP_X_REAL_IP", request.remote_addr),
         "weburl": payload.get("web_url"),
         "initial": payload.get("initial"),
         "reason": payload["reason"],
+        "species": payload["species"],
+        "categories": payload["categories"],
     }
 
     insert_query = """
@@ -76,14 +77,10 @@ def edit_wiki(comment_id: int):
         # Editing RDF:
         update_wiki_comment(
             comment_id=comment_id,
-            payload=payload,
-            next_version=next_version,
-            created=created,
-            sparql_conf={
-                "sparql_user": current_app.config["SPARQL_USER"],
-                "sparql_password": current_app.config["SPARQL_PASSWORD"],
-                "sparql_auth_uri": current_app.config["SPARQL_AUTH_URI"],
-            },
+            insert_dict=insert_dict,
+            sparql_user=current_app.config["SPARQL_USER"],
+            sparql_password=current_app.config["SPARQL_PASSWORD"],
+            sparql_auth_uri=current_app.config["SPARQL_AUTH_URI"]
         )
         return jsonify({"success": "ok"})
     return jsonify(error="Error editing wiki entry, most likely due to DB error!"), 500
diff --git a/gn3/db/rdf/wiki.py b/gn3/db/rdf/wiki.py
index f19670a..f2030ca 100644
--- a/gn3/db/rdf/wiki.py
+++ b/gn3/db/rdf/wiki.py
@@ -186,11 +186,10 @@ CONSTRUCT {
 
 
 def update_wiki_comment(
-        comment_id: int,
-        payload: dict,
-        created: str,
-        next_version: int,
-        sparql_conf: dict,
+        insert_dict: dict,
+        sparql_user: str,
+        sparql_password: str,
+        sparql_auth_uri: str,
         graph: str = "<http://genenetwork.org>",
 ) -> tuple[str, int]:
     """Update a wiki comment by inserting a comment with the same
@@ -220,7 +219,7 @@ looks like:
             }
     }
     """
-    name = f"gn:wiki-{comment_id}-{next_version}"
+    name = f"gn:wiki-{insert_dict['Id']}-{insert_dict['versionId']}"
     comment_triple = Template("""$name rdf:label '''$comment'''@en ;
 rdf:type gnc:GNWikiEntry ;
 gnt:symbol "$symbol" ;
@@ -228,31 +227,31 @@ dct:identifier "$comment_id"^^xsd:integer ;
 dct:hasVersion "$next_version"^^xsd:integer ;
 dct:created "$created"^^xsd:datetime .
 """).substitute(
-        comment=payload["comment"],
-        name=name, symbol=payload['symbol'],
-        comment_id=comment_id, next_version=next_version,
-        created=created)
+        comment=insert_dict["comment"],
+        name=name, symbol=insert_dict['symbol'],
+        comment_id=insert_dict["Id"], next_version=insert_dict["versionId"],
+        created=insert_dict["createtime"])
     using = ""
-    if payload["email"]:
-        comment_triple += f"{name} foaf:mbox <{payload['email']}> .\n"
-    if payload["initial"]:
-        comment_triple += f"{name} gnt:initial \"{payload['initial']}\" .\n"
-    if payload["species"]:
+    if insert_dict["email"]:
+        comment_triple += f"{name} foaf:mbox <{insert_dict['email']}> .\n"
+    if insert_dict["initial"]:
+        comment_triple += f"{name} gnt:initial \"{insert_dict['initial']}\" .\n"
+    if insert_dict["species"]:
         comment_triple += f"{name} gnt:belongsToSpecies ?speciesId .\n"
         using = Template(
             """ USING $graph WHERE { ?speciesId gnt:shortName "$species" . } """).substitute(
-                graph=graph, species=payload["species"]
+                graph=graph, species=insert_dict["species"]
         )
-    if payload["reason"]:
-        comment_triple += f"{name} gnt:reason \"{payload['reason']}\" .\n"
-    if payload["web_url"]:
-        comment_triple += f"{name} foaf:homepage <{payload['web_url']}> .\n"
-    for pmid in payload["pubmed_ids"]:
+    if insert_dict["reason"]:
+        comment_triple += f"{name} gnt:reason \"{insert_dict['reason']}\" .\n"
+    if insert_dict["weburl"]:
+        comment_triple += f"{name} foaf:homepage <{insert_dict['weburl']}> .\n"
+    for pmid in insert_dict["PubMed_ID"].split():
         comment_triple += f"{name} dct:references pubmed:{pmid} .\n"
-    for category in payload["categories"]:
+    for category in insert_dict["categories"]:
         comment_triple += f'{name} gnt:belongsToCategory "{category}".\n'
 
-    res = update_rdf(
+    return update_rdf(
         query=Template(
             """
 $prefix
@@ -265,8 +264,7 @@ $comment_triple}
                 graph=graph,
                 comment_triple=comment_triple,
                 using=using),
-        sparql_user=sparql_conf["sparql_user"],
-        sparql_password=sparql_conf["sparql_password"],
-        sparql_auth_uri=sparql_conf["sparql_auth_uri"],
+        sparql_user=sparql_user,
+        sparql_password=sparql_password,
+        sparql_auth_uri=sparql_auth_uri,
     )
-    return (res, 200)