From 3664f444d124a486274b3fbfaaca65daddf474cc Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 10 Oct 2023 19:54:57 +0300
Subject: Derive RDF_PREFIXES string from PREFIXES.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 gn3/db/rdf.py | 45 +++++++++++++++++++++++----------------------
 1 file changed, 23 insertions(+), 22 deletions(-)

(limited to 'gn3')

diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py
index b9cb468..521c2b7 100644
--- a/gn3/db/rdf.py
+++ b/gn3/db/rdf.py
@@ -12,29 +12,30 @@ from SPARQLWrapper import JSON, SPARQLWrapper
 
 from gn3.monads import MonadicDict
 
+PREFIXES = {
+    "dct": "http://purl.org/dc/terms/",
+    "ex": "http://example.org/stuff/1.0/",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "generif": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=",
+    "genotype": "http://genenetwork.org/genotype/",
+    "gn": "http://genenetwork.org/id/",
+    "gnc": "http://genenetwork.org/category/",
+    "gnt": "http://genenetwork.org/term/",
+    "owl": "http://www.w3.org/2002/07/owl#",
+    "phenotype": "http://genenetwork.org/phenotype/",
+    "publication": "http://genenetwork.org/publication/",
+    "pubmed": "http://rdf.ncbi.nlm.nih.gov/pubmed/",
+    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "skos": "http://www.w3.org/2004/02/skos/core#",
+    "taxon": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=",
+    "up": "http://purl.uniprot.org/core/",
+    "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+}
 
-RDF_PREFIXES = """
-PREFIX dcat: <http://www.w3.org/ns/dcat#>
-PREFIX dct: <http://purl.org/dc/terms/>
-PREFIX ex: <http://example.org/stuff/1.0/>
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
-PREFIX genotype: <http://genenetwork.org/genotype/>
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX gnt: <http://genenetwork.org/term/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX phenotype: <http://genenetwork.org/phenotype/>
-PREFIX publication: <http://genenetwork.org/publication/>
-PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-PREFIX taxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>
-PREFIX up: <http://purl.uniprot.org/core/>
-PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-"""
+
+RDF_PREFIXES = "\n".join([f"PREFIX {key}: <{value}>"for key, value in PREFIXES.items()])
 
 
 def sparql_query(
-- 
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