"""Sparql queries to get metadata about WIKI and RIF metadata. """ from string import Template from gn3.db.rdf import (BASE_CONTEXT, RDF_PREFIXES, query_frame_and_compact) 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): """Make sure `categories` and `pubmed_ids` are always arrays """ categories = result.get("categories") if isinstance(categories, str): result["categories"] = [categories] if categories else [] 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"]] return result def get_wiki_entries_by_symbol(symbol: str, sparql_uri: 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(""" $prefix CONSTRUCT { ?comment rdfs:label ?symbolName; gnt:reason ?reason ; gnt:species ?species ; dct:references ?pmid ; foaf:homepage ?weburl ; rdfs:comment ?text ; foaf:mbox ?email ; gnt:initial ?usercode ; gnt:belongsToCategory ?category ; gnt:hasVersion ?max ; dct:created ?created ; dct:identifier ?id_ . } WHERE { ?symbolId rdfs:label ?symbolName . ?comment rdfs:label ?text_ ; gnt:symbol ?symbolId ; rdf:type gnc:GNWikiEntry ; dct:identifier ?id_ ; dct:created ?createTime . FILTER ( LCASE(?symbolName) = LCASE('$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, symbol=symbol,) results = query_frame_and_compact( query, WIKI_CONTEXT, sparql_uri ) data = [__sanitize_result(result) for result in results.get("data")] 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) -> 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 . } WHERE { ?symbolId rdfs:label ?symbolName . ?comment rdf:type gnc:GNWikiEntry ; rdfs:label ?text_ ; gnt:symbol ?symbolId ; dct:created ?createTime ; dct:hasVersion ?version ; dct:identifier $comment_id ; dct:identifier ?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, comment_id=comment_id) results = query_frame_and_compact( query, WIKI_CONTEXT, sparql_uri ) data = [__sanitize_result(result) for result in results.get("data")] # We manually sort the array, since 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: # # results["data"] = sorted(data, key=lambda d: d["version"], reverse=True) return results