diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/rdf/wiki.py | 97 |
1 files changed, 96 insertions, 1 deletions
diff --git a/gn3/db/rdf/wiki.py b/gn3/db/rdf/wiki.py index c278ed8..152b261 100644 --- a/gn3/db/rdf/wiki.py +++ b/gn3/db/rdf/wiki.py @@ -9,8 +9,16 @@ NOTE: In the CONSTRUCT queries below, we manually sort the arrays from <https://stackoverflow.com/questions/78186393> <https://www.w3.org/TR/rdf-sparql-query/#modOrderBy> """ +import datetime + from string import Template -from gn3.db.rdf import BASE_CONTEXT, RDF_PREFIXES, query_frame_and_compact, sparql_query +from gn3.db.rdf import ( + BASE_CONTEXT, + RDF_PREFIXES, + query_frame_and_compact, + sparql_query, + update_rdf, +) from gn3.db.wiki import MissingDBDataException @@ -201,3 +209,90 @@ SELECT MAX(?version) as ?max_version FROM $graph WHERE { if not results: raise MissingDBDataException return int(results["max_version"]["value"]) + 1 + + +def update_wiki_comment( + comment_id: int, + payload: dict, + sparql_conf: dict, + graph: str = "<http://genenetwork.org>", +) -> tuple[str, int]: + """Update a wiki comment by inserting a comment with the same +identifier but an updated version id. The End form of this query +looks like: + + INSERT { + GRAPH <http://genenetwork.org> { + [ rdfs:label '''XXXX'''@en] rdf:type gnc:GNWikiEntry ; + gnt:symbol "XXXX" ; + foaf:mbox <XXXX> ; + gnt:initial "XXXX" ; + gnt:belongsToSpecies ?speciesId ; + gnt:reason "XXXX" ; + foaf:homepage <XXXX> ; + dct:references pmid:XXXX ; + dct:references pmid:XXXX ; + gnt:belongsToCategory "XXXX"; + gnt:belongsToCategory "XXXX"; + dct:hasVersion "123"^^xsd:integer ; + dct:identifier "1"^^xsd:integer ; + dct:created "2024-09-11 11:00"^^xsd:datetime . + + } USING <http://genenetwork.org> WHERE { + ?speciesId gnt:shortName "{species}" . + + } + } + """ + next_version = get_next_comment_version( + comment_id, sparql_conf['sparql_uri'], graph) + name = f"gn:wiki-{comment_id}-{next_version}" + comment_triple = Template("""$name rdf:label '''$comment'''@en ; +rdf:type gnc:GNWikiEntry ; +gnt:symbol "$symbol" ; +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=datetime.datetime.now(datetime.timezone.utc).strftime('%Y-%m-%d %H:%M:%S')) + 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"]: + comment_triple += f"{name} gnt:belongsToSpecies ?speciesId .\n" + using = Template( + """ USING $graph WHERE { ?speciesId gnt:shortName "$species" . } """).substitute( + graph=graph, species=payload["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"]: + comment_triple += f"{name} dct:references pubmed:{pmid} .\n" + for category in payload["categories"]: + comment_triple += f'{name} gnt:belongsToCategory "{category}".\n' + + res = update_rdf( + query=Template( + """ +$prefix + +INSERT { +GRAPH $graph { +$comment_triple} +} $using +""").substitute(prefix=RDF_PREFIXES, + 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"], + ) + return (res, 200) |