diff options
| -rw-r--r-- | gn3/db/rdf/wiki.py | 145 |
1 files changed, 78 insertions, 67 deletions
diff --git a/gn3/db/rdf/wiki.py b/gn3/db/rdf/wiki.py index f7bec47..2e397a8 100644 --- a/gn3/db/rdf/wiki.py +++ b/gn3/db/rdf/wiki.py @@ -21,10 +21,6 @@ WIKI_CONTEXT = BASE_CONTEXT | { "comment": "rdfs:comment", "created": "dct:created", "id": "dct:identifier", - # This points to the RDF Node which is the unique identifier - # for this triplet. It's constructed using the comment-id and - # the comment-versionId - "wiki_identifier": "@id", } @@ -36,51 +32,53 @@ def get_wiki_entries_by_symbol(symbol: str, sparql_uri: str) -> dict: $prefix CONSTRUCT { - ?uid rdfs:label ?symbolName; - gnt:reason ?reason ; - gnt:species ?species ; - dct:references ?pmid ; - foaf:homepage ?weburl ; - rdfs:comment ?comment ; - foaf:mbox ?email ; - gnt:initial ?usercode ; - gnt:belongsToCategory ?category ; - gnt:hasVersion ?versionId ; - dct:created ?created ; - dct:identifier ?identifier . + ?comment rdfs:label ?symbolName; + gnt:reason ?reason ; + gnt:species ?species ; + dct:references ?pmid ; + foaf:homepage ?weburl ; + rdfs:comment ?text ; + foaf:mbox ?email ; + gnt:initial ?usercode ; + gnt:belongsToCategory ?category ; + gnt:hasVersion ?max ; + dct:created ?created ; + dct:identifier ?id_ . } WHERE { ?symbolId rdfs:label ?symbolName . - ?uid rdfs:comment ?comment ; - gnt:symbol ?symbolId ; - rdf:type gnc:GNWikiEntry ; - dct:created ?createTime . + ?comment rdfs:label ?text_ ; + gnt:symbol ?symbolId ; + rdf:type gnc:GNWikiEntry ; + dct:identifier ?id_ ; + dct:created ?createTime . FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) . { SELECT (MAX(?vers) AS ?max) ?id_ WHERE { - ?symbolId rdfs:label ?symbolName . - ?uid dct:identifier ?id_ ; - dct:hasVersion ?vers ; - dct:identifier ?id_ ; - gnt:symbol ?symbolId . - FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) . + ?comment dct:identifier ?id_ ; + dct:hasVersion ?vers . } } - ?uid dct:hasVersion ?max ; - dct:identifier ?id_ . - OPTIONAL { ?uid gnt:reason ?reason } . + ?comment dct:hasVersion ?max . + OPTIONAL { ?comment gnt:reason ?reason_ } . OPTIONAL { - ?uid gnt:belongsToSpecies ?speciesId . + ?comment gnt:belongsToSpecies ?speciesId . ?speciesId gnt:shortName ?species . } . - OPTIONAL { ?uid dct:references ?pubmedId . } . - OPTIONAL { ?uid foaf:homepage ?weburl . } . - OPTIONAL { ?uid gnt:initial ?usercode . } . - OPTIONAL { ?uid foaf:mbox ?email . } . - OPTIONAL { ?uid gnt:belongsToCategory ?category . } . - BIND (str(?version) AS ?versionId) . - BIND (str(?id_) AS ?identifier) . - BIND (str(?pubmedId) AS ?pmid) . + 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( @@ -88,6 +86,18 @@ CONSTRUCT { sparql_uri ) data = results.get("data") + for result in data: + categories = result.get("categories") or [] + if categories and isinstance(categories, str): + result["categories"] = [categories] + pmids = result.get("pubmed_ids") + if pmids and isinstance(pmids, str): + result["pubmed_ids"] = [pmids] + elif pmids: + result["pubmed_ids"] = [int(pmid.split("/")[-1]) for pmid in pmids] + else: + result["pubmed_ids"] = [] + results["data"] = sorted(data, key=lambda d: d["created"]) if not data: return results return results @@ -99,42 +109,43 @@ def get_comment_history(comment_id: int, sparql_uri: str) -> dict: $prefix CONSTRUCT { - ?uid rdfs:label ?symbolName ; - gnt:reason ?reason ; - gnt:species ?species ; - dct:references ?pmid ; - foaf:homepage ?weburl ; - rdfs:comment ?comment ; - foaf:mbox ?email ; - gnt:initial ?usercode ; - gnt:belongsToCategory ?category ; - gnt:hasVersion ?versionId ; - dct:created ?created . + ?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 . - ?uid rdf:type gnc:GNWikiEntry ; - rdfs:comment ?comment ; - gnt:symbol ?symbolId ; - dct:created ?createTime ; - dct:hasVersion ?version ; - dct:identifier $comment_id ; - dct:identifier ?id_ . - OPTIONAL { ?uid gnt:reason ?reason_ } . + ?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 { - ?uid gnt:belongsToSpecies ?speciesId . + ?comment gnt:belongsToSpecies ?speciesId . ?speciesId gnt:shortName ?species_ . } . - OPTIONAL { ?uid dct:references ?pmid . } . - OPTIONAL { ?uid foaf:homepage ?weburl_ . } . - OPTIONAL { ?uid gnt:initial ?usercode_ . } . - OPTIONAL { ?uid foaf:mbox ?email_ . } . - OPTIONAL { ?uid gnt:belongsToCategory ?category_ . } . - BIND (str(?version) AS ?versionId) . + 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 (COALESCE(?weburl_, "") AS ?weburl) . + BIND (STR(COALESCE(?weburl_, "")) AS ?weburl) . BIND (COALESCE(?usercode_, "") AS ?usercode) . - BIND (COALESCE(?email_, "") AS ?email) . + BIND (STR(COALESCE(?email_, "")) AS ?email) . BIND (COALESCE(?species_, "") AS ?species) . BIND (COALESCE(?category_, "") AS ?category) . } @@ -152,7 +163,7 @@ CONSTRUCT { if pmids and isinstance(pmids, str): result["pubmed_ids"] = [pmids] elif pmids: - result["pubmed_ids"] = [int(pmid) for pmid in pmids] + result["pubmed_ids"] = [int(pmid.split("/")[-1]) for pmid in pmids] else: result["pubmed_ids"] = [] result["version"] = int(result["version"]) |