Merge pull request #69 from KNowledgeOnWebScale/EDC_active

fixed link-traversal example queries and small login error

Author: ecrum19

demonstrator/federated-automated-rhea-13.rq

@@ -0,0 +1,21 @@
+# Datasources: https://sparql.rhea-db.org/sparql https://sparql.uniprot.org/sparql/
+PREFIX rh: <http://rdf.rhea-db.org/>
+PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+PREFIX up: <http://purl.uniprot.org/core/>
+# Query 13
+# Select all Rhea reactions used to annotate Escherichia coli (taxid=83333) in UniProtKB/Swiss-Prot
+# return the number of UniProtKB entries
+SELECT ?uniprot ?mnemo ?rhea ?accession ?equation 
+WHERE {
+	{
+    VALUES (?taxid) { (taxon:83333) }
+    GRAPH <http://sparql.uniprot.org/uniprot> {
+      ?uniprot up:reviewed true . 
+      ?uniprot up:mnemonic ?mnemo . 
+      ?uniprot up:organism ?taxid .
+      ?uniprot up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea . 
+    }
+  }
+  ?rhea rh:accession ?accession .
+  ?rhea rh:equation ?equation .
+}

demonstrator/link-traversal-solidbench-1.rq

@@ -0,0 +1,11 @@
+# Datasources: https://solidbench.linkeddatafragments.org/pods/00000000000000000933/profile/card
+# QueryMode: solid-link-traversal
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX snvoc: <https://solidbench.linkeddatafragments.org/www.ldbc.eu/ldbc_socialnet/1.0/vocabulary/>
+SELECT ?messageId ?messageCreationDate ?messageContent WHERE {
+  ?message snvoc:hasCreator <https://solidbench.linkeddatafragments.org/pods/00000000000000000933/profile/card#me>;
+    rdf:type snvoc:Post;
+    snvoc:content ?messageContent;
+    snvoc:creationDate ?messageCreationDate;
+    snvoc:id ?messageId.
+}

demonstrator/link-traversal-solidbench-2.rq

@@ -0,0 +1,10 @@
+# Datasources: https://solidbench.linkeddatafragments.org/pods/00000015393162789111/posts
+# QueryMode: solid-link-traversal
+PREFIX snvoc: <https://solidbench.linkeddatafragments.org/www.ldbc.eu/ldbc_socialnet/1.0/vocabulary/>
+SELECT ?personId ?firstName ?lastName WHERE {
+  <https://solidbench.linkeddatafragments.org/pods/00000015393162789111/posts#893353506423> snvoc:id ?messageId;
+    snvoc:hasCreator ?creator.
+  ?creator snvoc:id ?personId;
+    snvoc:firstName ?firstName;
+    snvoc:lastName ?lastName.
+}

demonstrator/solid-link-traversal-foaf-knows.rq

@@ -1,4 +1,4 @@
-# Datasources: https://triple.ilabt.imec.be/test/bio-usecase/nbn-chist-era-annex-1-chemicals-custom-predicate.ttl
+# Datasources: https://triple.ilabt.imec.be/test/
 # QueryMode: solid-no-traversal
 SELECT ?s ?p ?o
 WHERE {

demonstrator/solid-link-traversal-see-also.rq

@@ -1,4 +1,4 @@
-# Datasources: http://localhost:3000/test/random/nbn-chist-era-annex-1-chemicals-custom-predicate.ttl
+# Datasources: https://triple.ilabt.imec.be/test/bio-usecase/nbn-chist-era-annex-1-chemicals-custom-predicate.ttl
 # QueryMode: solid-no-traversal
 PREFIX thd: <urn:triple-hybrid-demo:>
 SELECT DISTINCT ?CAS WHERE {

demonstrator/solid-no-traversal-basic-select.rq

@@ -2245,6 +2245,23 @@ export default {
     isLikelySolidOrRdfSource(source: string) {
       return !this.isLikelySparqlEndpointSource(source);
     },
+    /**
+     * Infers query mode from canonical example filename prefixes so the sample
+     * picker remains stable even when files omit explicit # QueryMode metadata.
+     */
+    inferModeFromExampleId(exampleId: string): QueryExecutionMode | null {
+      const normalizedId = exampleId.toLowerCase();
+      if (
+        normalizedId.startsWith("link-traversal-") ||
+        normalizedId.startsWith("link-taversal-")
+      ) {
+        return "solid-link-traversal";
+      }
+      if (normalizedId.startsWith("solid-no-traversal-")) {
+        return "solid-no-traversal";
+      }
+      return null;
+    },
     /**
      * Determines the target query engine mode for an example query. Authors can
      * explicitly pin a mode via `# QueryMode: <mode-id>` in the .rq file.
@@ -2253,6 +2270,7 @@ export default {
       _queryText: string,
       sources: string[],
       declaredMode?: string,
+      exampleId?: string,
     ): QueryExecutionMode {
       if (
         declaredMode &&
@@ -2261,6 +2279,13 @@ export default {
         return declaredMode as QueryExecutionMode;
       }
 
+      if (exampleId) {
+        const modeFromName = this.inferModeFromExampleId(exampleId);
+        if (modeFromName) {
+          return modeFromName;
+        }
+      }
+
       const endpointSourceCount = sources.filter((source) =>
         this.isLikelySparqlEndpointSource(source),
       ).length;
@@ -2283,6 +2308,7 @@ export default {
       queryText: string,
       sources: string[],
       mode: QueryExecutionMode,
+      exampleId?: string,
     ): ExampleQueryCategory {
       if (mode === "solid-link-traversal") {
         return "Solid query (link traversal)";
@@ -2291,13 +2317,32 @@ export default {
         return "Solid query (no traversal)";
       }
 
+      const normalizedId = (exampleId || "").toLowerCase();
+      if (normalizedId.startsWith("federated-")) {
+        return "Federated query";
+      }
+
       const hasServiceClause = /service\s*<[^>]+>/i.test(queryText);
       const endpointSourceCount = sources.filter((source) =>
         this.isLikelySparqlEndpointSource(source),
       ).length;
+      const endpointHosts = new Set(
+        sources
+          .filter((source) => this.isLikelySparqlEndpointSource(source))
+          .map((source) => this.normalizeSourceUrlForValidation(source))
+          .map((source) => {
+            try {
+              return new URL(source).host;
+            } catch {
+              return "";
+            }
+          })
+          .filter((host) => host.length > 0),
+      );
 
       if (
         hasServiceClause ||
+        endpointHosts.size > 1 ||
         endpointSourceCount > 1 ||
         (endpointSourceCount === 1 && sources.length > 1)
       ) {
@@ -2576,8 +2621,14 @@ export default {
           query,
           sources,
           declaredMode,
+          rawName,
+        );
+        const category = this.categorizeExampleQuery(
+          query,
+          sources,
+          mode,
+          rawName,
         );
-        const category = this.categorizeExampleQuery(query, sources, mode);
         queries.push({
           id: rawName,
           name,
@@ -2604,8 +2655,10 @@ export default {
       );
       if (!example) return;
 
-      // Clone example sources so user edits never mutate the static sample list.
-      this.currentQuery.sources = [...example.sources];
+      // Link-traversal examples intentionally start with no explicit datasource.
+      // Comunica can derive traversal seeds from IRIs that appear in the query.
+      this.currentQuery.sources =
+        example.mode === "solid-link-traversal" ? [] : [...example.sources];
       this.currentQuery.query = example.query || "";
       this.queryMode = example.mode;
       this.syncYasqeFromExternalQuery(this.currentQuery.query, {

demonstrator/triple-solid-2.rq

@@ -52,12 +52,12 @@
             Targets multiple SPARQL endpoints in one execution (commonly via SERVICE clauses).
           </li>
           <li>
-            <span class="guide-tag">Solid query</span>
-            Targets RDF resources from a Solid pod or local server.
+            <span class="guide-tag">Solid query (no traversal)</span>
+            Targets explicit Solid RDF resources/containers without discovering linked documents.
           </li>
           <li>
-            <span class="guide-tag">Mixed source federated query</span>
-            Targets both Solid pod sources and SPARQL endpoint sources.
+            <span class="guide-tag">Solid query (link traversal)</span>
+            Starts from Solid seed URLs and discovers additional RDF documents by following links.
           </li>
         </ul>
       </section>
@@ -70,6 +70,22 @@
             <span class="guide-control">baseline-test</span>
             Quick concept-check query on the Rhea endpoint that returns a small set of predicate IRIs.
           </li>
+          <li>
+            <span class="guide-control">federated-automated-rhea-13</span>
+            Federates UniProt and Rhea to list E. coli-reviewed proteins and associated reactions.
+          </li>
+          <li>
+            <span class="guide-control">federated-uniprot-rhea-human-reactions</span>
+            Fetches human proteins in UniProt and joins to reaction labels from Rhea.
+          </li>
+          <li>
+            <span class="guide-control">federated-wikidata-uniprot-human-proteins</span>
+            Uses Wikidata + UniProt federation to enrich proteins with mnemonics.
+          </li>
+          <li>
+            <span class="guide-control">federated-wikidata-cities</span>
+            Single-endpoint Wikidata city query with label service for readable output.
+          </li>
           <li>
             <span class="guide-control">triple-wikidata-1</span>
             Aggregates toxicity-related compound data in Wikidata and ranks by average LD50.
@@ -95,8 +111,20 @@
             Retrieves OMA ortholog protein links and organism names for a selected UniProt protein.
           </li>
           <li>
-            <span class="guide-control">triple-combined-service</span>
-            Full mixed-source federated workflow that chains Solid/local CAS data, IDSM similarity search, and Rhea reactions.
+            <span class="guide-control">solid-no-traversal-basic-select</span>
+            Reads triples directly from a selected Solid container without traversal.
+          </li>
+          <li>
+            <span class="guide-control">solid-no-traversal-literal-preview</span>
+            Extracts literal values from a specific Solid RDF document.
+          </li>
+          <li>
+            <span class="guide-control">link-traversal-solidbench-1</span>
+            SolidBench link-traversal query that starts at a profile seed and discovers related posts.
+          </li>
+          <li>
+            <span class="guide-control">link-traversal-solidbench-2</span>
+            SolidBench link-traversal query that resolves creator details from a message seed URL.
           </li>
         </ul>
       </section>