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-rw-r--r--gn3/db/rdf/wiki.py145
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"])
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 08:36:13 +0000