Restructure RDF module.

* gn3/api/metadata.py: Import constants from gn3.db.rdf
* gn3/api/metadata_api/wiki.py: Ditto.  Import
"get_wiki_entries_by_symbol" from gn3.db.rdf.wiki.
* gn3/db/constants.py: Delete file and move all constants ...
* gn3/db/rdf.py: ... and functions ...
* gn3/db/rdf/__init__.py: ... here.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 91 insertions, 0 deletions

diff --git a/gn3/db/rdf/wiki.py b/gn3/db/rdf/wiki.py
new file mode 100644
index 0000000..1fc3130
--- /dev/null
+++ b/gn3/db/rdf/wiki.py
@@ -0,0 +1,91 @@
+"""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)
+
+
+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("""
+$prefix
+
+CONSTRUCT {
+    ?uid rdfs:label ?symbolName;
+         gnt:reason ?reason ;
+         gnt:species ?species ;
+         dct:references ?pmid ;
+         foaf:homepage ?weburl ;
+         rdfs:comment ?comment ;
+         foaf:mbox ?email ;
+         gnt:initial ?usercode ;
+         gnt:belongsToCategory ?category ;
+         gnt:hasVersion ?versionId ;
+         dct:created ?created ;
+         dct:identifier ?identifier .
+} WHERE {
+    ?symbolId rdfs:label ?symbolName .
+    ?uid rdfs:comment ?comment ;
+         gnt:symbol ?symbolId ;
+         rdf:type gnc:GNWikiEntry ;
+         dct:created ?createTime .
+    FILTER ( LCASE(?symbolName) = LCASE('$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') ) .
+        }
+    }
+    ?uid dct:hasVersion ?max ;
+         dct:identifier ?id_ .
+    OPTIONAL { ?uid gnt:reason ?reason } .
+    OPTIONAL {
+        ?uid gnt:belongsToSpecies ?speciesId .
+        ?speciesId gnt:shortName ?species .
+    } .
+    OPTIONAL { ?uid dct:references ?pubmedId . } .
+    OPTIONAL { ?uid foaf:homepage ?weburl . } .
+    OPTIONAL { ?uid gnt:initial ?usercode . } .
+    OPTIONAL { ?uid gnt:mbox ?email . } .
+    OPTIONAL { ?uid gnt:belongsToCategory ?category . } .
+    BIND (str(?version) AS ?versionId) .
+    BIND (str(?id_) AS ?identifier) .
+    BIND (str(?pubmedId) AS ?pmid) .
+    BIND (str(?createTime) AS ?created) .
+}
+""").substitute(prefix=RDF_PREFIXES, symbol=symbol,)
+    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_id": "dct:references",
+        "email": "foaf:mbox",
+        "initial": "gnt:initial",
+        "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",
+    }
+    results = query_frame_and_compact(
+        query, context,
+        sparql_uri
+    )
+    data = results.get("data")
+    if not data:
+        return results
+    return results