fixed BASE URI for SPARQL queries

SouthGreenPlatform · Aug 30, 2024 · edf34a0 · edf34a0
1 parent 78d18cd
commit edf34a0
Showing 1 changed file with 29 additions and 16 deletions.
diff --git a/agrold-javaweb/src/main/java/agrold/webservices/dao/TaxonDAO.java b/agrold-javaweb/src/main/java/agrold/webservices/dao/TaxonDAO.java
@@ -12,24 +12,37 @@
 public class TaxonDAO {
 
     public static final String TAXON_TYPE_URI2 = "http://purl.obolibrary.org/obo/NCBITaxon_species";
-    public static final String TAXON_TYPE_URI = "http://www.southgreen.fr/agrold/resource/Taxon";
+    public static final String TAXON_TYPE_URI = "http://purl.agrold.org/vocabulary/Taxon";
     public static final String[] TYPEURIs = new String[]{TAXON_TYPE_URI, TAXON_TYPE_URI2};
 
     // return URIs and agrold_vocabulary:description of all genes in Agrold
     public static String getTaxons(int page, int pageSize, String resultFormat) throws IOException {
 
-        String sparqlQuery = "PREFIX agrold:<http://www.southgreen.fr/agrold/vocabulary/> \n"
-                + "PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>\n"
-                + "PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
-                + "SELECT distinct ?taxonId ?taxonName (group_concat(distinct ?d;separator=\"; \") as ?Description) (?taxon AS ?URI)\n"
-                + "WHERE {\n"
-                + "    OPTIONAL {?taxon rdfs:label ?taxonName .}\n"
-                + "    OPTIONAL { ?taxon agrold:has_trait ?d} \n"
-                + "    ?taxon rdf:type|rdfs:subClassOf ?type.\n"
-                + "    FILTER(?type IN (<"+TAXON_TYPE_URI+">,<"+TAXON_TYPE_URI2+">))\n"
-                + "    BIND(REPLACE(str(?taxon), '^.*(#|/)', \"\") AS ?taxonId) .\n"
-                + "}\n"
-                + "ORDER BY DESC(?URI)";
+        // String sparqlQuery = "PREFIX agrold:<http://purl.agrold.org/vocabulary/> \n"
+        //         + "PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>\n"
+        //         + "PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
+        //         + "SELECT distinct ?taxonId ?taxonName (group_concat(distinct ?d;separator=\"; \") as ?Description) (?taxon AS ?URI)\n"
+        //         + "WHERE {\n"
+        //         + "    OPTIONAL {?taxon rdfs:label ?taxonName .}\n"
+        //         + "    OPTIONAL { ?taxon agrold:has_trait ?d} \n"
+        //         + "    ?taxon rdf:type|rdfs:subClassOf ?type.\n"
+        //         + "    FILTER(?type IN (<"+TAXON_TYPE_URI+">,<"+TAXON_TYPE_URI2+">))\n"
+        //         + "    BIND(REPLACE(str(?taxon), '^.*(#|/)', \"\") AS ?taxonId) .\n"
+        //         + "}\n"
+        //         + "ORDER BY DESC(?URI)";
+        String sparqlQuery = "BASE <http://purl.agrold.org/>\n"
+        + "PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
+        + "PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>\n"
+        + "PREFIX fn:<https://www.w3.org/TR/xpath-functions-31/#>\n"
+        + "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n"
+        + "PREFIX graph: <ensembl.plants>\n"
+        + "SELECT distinct ?species\n"
+        + "WHERE { \n"
+        + "values (?q){(<http://purl.obolibrary.org/obo/RO_0002162>)}\n"
+        + "graph graph:{ \n"
+        + " ?gene ?q ?species . \n"
+        + "} \n"
+        + "} \n";
         sparqlQuery = Utils.addLimitAndOffset(sparqlQuery, pageSize, page);
 
         return Utils.executeSparqlQuery(sparqlQuery, Utils.sparqlEndpointURL, resultFormat);
@@ -62,7 +75,7 @@ public static String getTaxonIdAssociatedWithOntoId(String ontoId, int page, int
 //                + "    BIND(REPLACE(str(?taxon), '^.*(#|/)', \"\") AS ?taxonId) .\n"
 //                + "  }\n"
 //                + "}";
-        String sparqlQuery = "BASE <http://www.southgreen.fr/agrold/>\n"
+        String sparqlQuery = "BASE <http://purl.agrold.org/>\n"
                 + "PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
                 + "PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>\n"
                 + "SELECT DISTINCT ?taxonId (?taxon AS ?URI) ?taxonLabel (REPLACE(str(?predicate), '^.*(#|/)', \"\") AS ?Association) "
@@ -72,7 +85,7 @@ public static String getTaxonIdAssociatedWithOntoId(String ontoId, int page, int
                 + "  {\n"
                 + "    ?taxon ?predicate ?ontoElt .\n"
                 + "    ?ontoElt rdfs:subClassOf ?ontoEltClass.\n"
-                + "    {?taxon rdf:type <http://www.southgreen.fr/agrold/resource/Taxon>.}\n"
+                + "    {?taxon rdf:type <http://purl.agrold.org/vocabulary/Taxon>.}\n"
                 + "    UNION\n"
                 + "    {?taxon rdfs:subClassOf <http://purl.obolibrary.org/obo/SO_0000771>.}\n"
                 + "    optional {?ontoElt rdfs:label ?ontoLabel}\n"
@@ -88,7 +101,7 @@ public static String getTaxonIdAssociatedWithOntoId(String ontoId, int page, int
     }
 
     public static String getTaxonsAssociatedWithProteinId(String proteinId, int page, int pageSize, String resultFormat) throws IOException {
-        String sparqlQuery = "BASE <http://www.southgreen.fr/agrold/>\n"
+        String sparqlQuery = "BASE <http://purl.agrold.org/>\n"
                 + "PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>\n"
                 + "PREFIX vocab:<vocabulary/>\n"
                 + "PREFIX graph1:<protein.annotations>\n"