Set wikidata prefixes to an IRI for now.

Don't try to add a comment just put a TODO

src/main/java/swiss/sib/rdf/sparql/examples/Fixer.java

@@ -167,7 +167,8 @@ private Map<String, String> loadPrefixes() throws IOException {
 
 	private void fix(IRI queryIri, Value query, Path file, Model model, Map<String, String> prefixes2) {
 		String queryIriStr = queryIri.stringValue();
-		String queryStr = query.stringValue();
+		String queryStr = query.stringValue()
+				.replace("\\\"", "\"");
 
 
 		String fixedPrefixes = Fixer.fixMissingPrefixes(queryStr, prefixes2);

src/main/java/swiss/sib/rdf/sparql/examples/Wikibase.java

@@ -81,6 +81,8 @@ public class Wikibase implements Callable<Integer> {
 	private File outputHtmlDir;
 	private static final ValueFactory VF = SimpleValueFactory.getInstance();
 
+	private static final IRI WIKIDATA_PREFIXES = VF.createIRI("https://example.org/to_decide/wikidata_prefixes");
+
 	private static final IRI CC_BY_4 = VF.createIRI("https://creativecommons.org/licenses/by-sa/4.0/");
 
 	public Integer call() {
@@ -108,7 +110,7 @@ public Integer call() {
 	}
 
 	private enum NamedTemplate {
-		SPARQL("SPARQL", ".mw-highlight-lang-sparql"), 
+		SPARQL("SPARQL", ".mw-highlight-lang-sparql"),
 //		WDQUERY("Wdquery", ".mw-highlight-lang-sparql"),
 //		SPARQL_INLINE("SPARQL_Inline/doc", ".mw-highlight-lang-sparql"),
 		SPARQL2("SPARQL2", ".mw-highlight-lang-sparql"),;
@@ -129,7 +131,7 @@ private void fetchHtml() {
 			String url = wikidatawiki + "w/index.php?title=Special:WhatLinksHere/Template:" + nt.name;
 
 			try {
-				while (url != null) {
+				while (url != null && !url.equals(wikidatawiki)) {
 					Document searchResultDocument = retrieveAndCacheResult(url, outputSearchResultDir);
 					Elements ulWhatLinksHereList = searchResultDocument.select("#mw-whatlinkshere-list li > a");
 					for (Element link : ulWhatLinksHereList) {
@@ -150,7 +152,8 @@ private String makeAbsoluteUrl(Element link) {
 		String pageLinkingToSparqlTemplate = link.attr("href");
 		if (pageLinkingToSparqlTemplate.startsWith("/")) {
 			pageLinkingToSparqlTemplate = wikidatawiki + pageLinkingToSparqlTemplate;
-		}
+		} else if (pageLinkingToSparqlTemplate == null || pageLinkingToSparqlTemplate.isBlank())
+			return null;
 		return pageLinkingToSparqlTemplate;
 	}
 
@@ -167,27 +170,34 @@ private void extractSparqlQueriesFromPage(String pageLinkingToSparqlTemplate, Na
 
 			Elements sparqlTemplates = htmlPageDocument.select(nt.cssClass);
 			for (Element sparqlTemplate : sparqlTemplates) {
-				String query = sparqlTemplate.select("pre").eachText().stream().collect(Collectors.joining("\n"));
+				//Concat the SPARQL string undo " escaping.
+				String query = sparqlTemplate.select("pre").eachText().stream().collect(Collectors.joining("\n"))
+						.replace("\\\"", "\"");
 				LinkedHashModel model = new LinkedHashModel();
 
 				String urlForFileName = new MD5().evaluate(VF, VF.createLiteral(query)).stringValue();
 				IRI iriForQuery = VF.createIRI(wikidatawiki + "#query-" + urlForFileName);
 				addQueryStringToModel(query, model, iriForQuery);
-				StringBuilder sb = makeThePreviosSiblingNodesTheLabel(sparqlTemplate);
-				if (!sb.isEmpty() && languageInHtml != null && !languageInHtml.isBlank()) {
-					model.add(iriForQuery, RDFS.COMMENT, VF.createLiteral(sb.toString(), languageInHtml));
-				} else if (!sb.isEmpty()) {
-					model.add(iriForQuery, RDFS.COMMENT, VF.createLiteral(sb.toString()));
-				}
+				model.add(iriForQuery, RDFS.COMMENT, VF.createLiteral("TODO", "en"));
+//				extractComment(languageInHtml, sparqlTemplate, model, iriForQuery);
 				model.add(iriForQuery, DCTERMS.IS_PART_OF, VF.createIRI(pageLinkingToSparqlTemplate));
 				model.add(iriForQuery, DCTERMS.LICENSE, CC_BY_4);
-				model.add(iriForQuery, SHACL.PREFIXES, VF.createBNode("wikidata_prefixes"));
+				model.add(iriForQuery, SHACL.PREFIXES, WIKIDATA_PREFIXES);
 				model.add(iriForQuery, SchemaDotOrg.TARGET, VF.createIRI(wikidatasparql));
 				writeModelToTurtle(model, urlForFileName);
 			}
 		}
 	}
 
+	private void extractComment(String languageInHtml, Element sparqlTemplate, LinkedHashModel model, IRI iriForQuery) {
+		StringBuilder sb = makeThePreviosSiblingNodesTheLabel(sparqlTemplate);
+		if (!sb.isEmpty() && languageInHtml != null && !languageInHtml.isBlank()) {
+			model.add(iriForQuery, RDFS.COMMENT, VF.createLiteral(sb.toString(), languageInHtml));
+		} else if (!sb.isEmpty()) {
+			model.add(iriForQuery, RDFS.COMMENT, VF.createLiteral(sb.toString()));
+		}
+	}
+
 	private StringBuilder makeThePreviosSiblingNodesTheLabel(Element sparqlTemplate) {
 		Element parent = sparqlTemplate.parent();
 		List<Node> childNodes = parent.childNodes();

src/test/java/swiss/sib/rdf/sparql/examples/FixerTest.java

@@ -1,6 +1,7 @@
 package swiss.sib.rdf.sparql.examples;
 
 import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.fail;
 
 import java.util.Map;
@@ -37,6 +38,41 @@ public class FixerTest {
 			  INCLUDE %get_labels
 			  ?item a rdfs:Class .
 			}""";
+
+	private final String blazeGraphWithoutIncludeExample = """
+			PREFIX wikibase: <http://wikiba.se/ontology#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+PREFIX wd: <http://www.wikidata.org/entity/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX bd: <http://www.bigdata.com/rdf#>
+PREFIX geof: <http://www.opengis.net/def/function/geosparql/>
+SELECT
+  ?place
+  ?placeLabel
+  ?dist
+  (GROUP_CONCAT(DISTINCT ?instanceLabel; SEPARATOR = \", \") AS ?instanceLabels)
+  (GROUP_CONCAT(DISTINCT ?adminLabel; SEPARATOR = \", \") AS ?adminLabels)
+WHERE
+{
+  wd:Q116716361 wdt:P625 ?loc .
+  SERVICE wikibase:around {
+      ?place wdt:P625 ?location .
+      bd:serviceParam wikibase:center ?loc .
+      bd:serviceParam wikibase:radius \"6\" .
+  }
+  OPTIONAL { ?place wdt:P31 ?instance }
+  OPTIONAL { ?place wdt:P131 ?admin }
+  SERVICE wikibase:label {
+    bd:serviceParam wikibase:language \"en\" .
+    ?instance rdfs:label ?instanceLabel .
+    ?place rdfs:label ?placeLabel .
+    ?admin rdfs:label ?adminLabel .
+  }
+  BIND(geof:distance(?loc, ?location) as ?dist)
+}
+GROUP BY ?place ?placeLabel ?dist
+ORDER BY ?dist""";
+
 
 	@Test
 	public void simpleIncludeWith() {
@@ -50,6 +86,19 @@ public void simpleIncludeWith() {
 		}
 	}
 
+	@Test
+	public void real() {
+		try {
+			String fix = Fixer.fixBlazeGraphIncludeWith(blazeGraphWithoutIncludeExample, "", null);
+			assertNull(fix);
+
+			QueryParser parser = new SPARQLParserFactory().getParser();
+			parser.parseQuery(blazeGraphWithoutIncludeExample, "http://example.org/");
+		} catch (MalformedQueryException e) {
+			fail(e);
+		}
+	}
+
 	@Test
 	public void simpleMissingPrefix() {
 		try {