"""Sparql queries to get metadata about WIKI and RIF metadata. NOTE: In the CONSTRUCT queries below, we manually sort the arrays from the result of a CONSTRUCT. This is because the SPARQL engine does not provide a guarantee that it will support an ORDER BY clause in a CONSTRUCT. Using ORDER BY on a solution sequence for a CONSTRUCT or DESCRIBE query has no direct effect because only SELECT returns a sequence of results. See: """ from string import Template from gn3.db.rdf import ( BASE_CONTEXT, RDF_PREFIXES, query_frame_and_compact, update_rdf, ) WIKI_CONTEXT = BASE_CONTEXT | { "foaf": "http://xmlns.com/foaf/0.1/", "dct": "http://purl.org/dc/terms/", "categories": "gnt:belongsToCategory", "web_url": "foaf:homepage", "version": "gnt:hasVersion", "symbol": "rdfs:label", "reason": "gnt:reason", "species": "gnt:species", "pubmed_ids": "dct:references", "email": "foaf:mbox", "initial": "gnt:initial", "comment": "rdfs:comment", "created": "dct:created", "id": "dct:identifier", } def __sanitize_result(result: dict) -> dict: """Make sure `categories` and `pubmed_ids` are always arrays""" if not result: return {} categories = result.get("categories") if isinstance(categories, str): result["categories"] = [categories] if categories else [] result["categories"] = sorted(result["categories"]) pmids = result.get("pubmed_ids") if isinstance(pmids, str): result["pubmed_ids"] = [pmids] if pmids else [] if isinstance(pmids, int): result["pubmed_ids"] = [pmids] result["pubmed_ids"] = [ int(pmid.split("/")[-1]) if isinstance(pmid, str) else pmid for pmid in result["pubmed_ids"] ] result["pubmed_ids"] = sorted(result["pubmed_ids"]) return result def get_wiki_entries_by_symbol( symbol: str, sparql_uri: str, graph: str = "" ) -> dict: """Fetch all the Wiki entries using the symbol""" # This query uses a sub-query to fetch the latest comment by the # version id. query = Template( """ $prefix CONSTRUCT { ?comment rdfs:label ?symbol; gnt:reason ?reason ; gnt:species ?species ; dct:references ?pmid ; foaf:homepage ?weburl ; rdfs:comment ?text ; foaf:mbox ?email ; gnt:initial ?usercode ; gnt:belongsToCategory ?category ; gnt:hasVersion ?max ; dct:created ?created ; dct:identifier ?id_ . } FROM $graph WHERE { ?comment rdfs:label ?text_ ; gnt:symbol ?symbol ; rdf:type gnc:GNWikiEntry ; dct:identifier ?id_ ; dct:created ?createTime . FILTER ( LCASE(?symbol) = LCASE('$symbol') ) . { SELECT (MAX(?vers) AS ?max) ?id_ WHERE { ?comment dct:identifier ?id_ ; dct:hasVersion ?vers . } } ?comment dct:hasVersion ?max . OPTIONAL { ?comment gnt:reason ?reason_ } . OPTIONAL { ?comment gnt:belongsToSpecies ?speciesId . ?speciesId gnt:shortName ?species . } . OPTIONAL { ?comment dct:references ?pmid_ } . OPTIONAL { ?comment foaf:homepage ?weburl_ } . OPTIONAL { ?comment gnt:initial ?usercode_ } . OPTIONAL { ?comment foaf:mbox ?email_ } . OPTIONAL { ?comment gnt:belongsToCategory ?category_ } . BIND (str(?createTime) AS ?created) . BIND (str(?text_) AS ?text) . BIND (str(?version) AS ?versionId) . BIND (STR(COALESCE(?pmid_, "")) AS ?pmid) . BIND (COALESCE(?reason_, "") AS ?reason) . BIND (STR(COALESCE(?weburl_, "")) AS ?weburl) . BIND (COALESCE(?usercode_, "") AS ?usercode) . BIND (STR(COALESCE(?email_, "")) AS ?email) . BIND (COALESCE(?species_, "") AS ?species) . BIND (COALESCE(?category_, "") AS ?category) . } """ ).substitute( prefix=RDF_PREFIXES, graph=graph, symbol=symbol, ) results = query_frame_and_compact(query, WIKI_CONTEXT, sparql_uri) data = [__sanitize_result(result) for result in results.get("data", {})] # See note above in the doc-string results["data"] = sorted(data, key=lambda d: d["created"]) if not data: return results return results def get_comment_history( comment_id: int, sparql_uri: str, graph: str = "" ) -> dict: """Get all the historical data for a given id""" query = Template( """ $prefix CONSTRUCT { ?comment rdfs:label ?symbolName ; gnt:reason ?reason ; gnt:species ?species ; dct:references ?pmid ; foaf:homepage ?weburl ; rdfs:comment ?text ; foaf:mbox ?email ; gnt:initial ?usercode ; gnt:belongsToCategory ?category ; gnt:hasVersion ?version ; dct:created ?created . } FROM $graph WHERE { ?comment rdf:type gnc:GNWikiEntry ; rdfs:label ?text_ ; gnt:symbol ?symbol ; dct:created ?createTime ; dct:hasVersion ?version ; dct:identifier $comment_id . OPTIONAL { ?comment gnt:reason ?reason_ } . OPTIONAL { ?comment gnt:belongsToSpecies ?speciesId . ?speciesId gnt:shortName ?species_ . } . OPTIONAL { ?comment dct:references ?pmid_ . } . OPTIONAL { ?comment foaf:homepage ?weburl_ . } . OPTIONAL { ?comment gnt:initial ?usercode_ . } . OPTIONAL { ?comment foaf:mbox ?email_ . } . OPTIONAL { ?comment gnt:belongsToCategory ?category_ . } . BIND (str(?text_) AS ?text) . BIND (str(?createTime) AS ?created) . BIND (STR(COALESCE(?pmid_, "")) AS ?pmid) . BIND (COALESCE(?reason_, "") AS ?reason) . BIND (STR(COALESCE(?weburl_, "")) AS ?weburl) . BIND (COALESCE(?usercode_, "") AS ?usercode) . BIND (STR(COALESCE(?email_, "")) AS ?email) . BIND (COALESCE(?species_, "") AS ?species) . BIND (COALESCE(?category_, "") AS ?category) . } """ ).substitute(prefix=RDF_PREFIXES, graph=graph, comment_id=comment_id) results = query_frame_and_compact(query, WIKI_CONTEXT, sparql_uri) data = [__sanitize_result(result) for result in results.get("data", {})] # See note above in the doc-string results["data"] = sorted(data, key=lambda d: d["version"], reverse=True) return results def update_wiki_comment( insert_dict: dict, sparql_user: str, sparql_password: str, sparql_auth_uri: str, graph: str = "", ) -> str: """Update a wiki comment by inserting a comment with the same identifier but an updated version id. The End form of this query looks like: INSERT { GRAPH { [ rdfs:label '''XXXX'''@en] rdf:type gnc:GNWikiEntry ; gnt:symbol "XXXX" ; foaf:mbox ; gnt:initial "XXXX" ; gnt:belongsToSpecies ?speciesId ; gnt:reason "XXXX" ; foaf:homepage ; dct:references pmid:XXXX ; dct:references pmid:XXXX ; gnt:belongsToCategory "XXXX"; gnt:belongsToCategory "XXXX"; dct:hasVersion "123"^^xsd:integer ; dct:identifier "1"^^xsd:integer ; dct:created "2024-09-11 11:00"^^xsd:datetime . } USING WHERE { ?speciesId gnt:shortName "{species}" . } } """ name = f"gn:wiki-{insert_dict['Id']}-{insert_dict['versionId']}" comment_triple = Template("""$name rdf:label '''$comment'''@en ; rdf:type gnc:GNWikiEntry ; gnt:symbol "$symbol" ; dct:identifier "$comment_id"^^xsd:integer ; dct:hasVersion "$next_version"^^xsd:integer ; dct:created "$created"^^xsd:datetime . """).substitute( 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 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=insert_dict["species"] ) 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 insert_dict["categories"]: comment_triple += f'{name} gnt:belongsToCategory "{category}".\n' return 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_user, sparql_password=sparql_password, sparql_auth_uri=sparql_auth_uri, )