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-rw-r--r--gn3/api/metadata_api/wiki.py21
-rw-r--r--gn3/db/rdf/wiki.py52
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)