test quads

qendpoint-backend/src/main/java/com/the_qa_company/qendpoint/controller/Sparql.java

@@ -426,7 +426,7 @@ void initializeEndpointStore(boolean finishLoading) throws IOException {
 			CompiledSailOptions options = new CompiledSailOptions();
 			options.setPort(port);
 			options.setEndpointThreshold(threshold);
-			options.setHdtSpec(hdtSpec);
+			options.setHdtSpec(HDTOptions.of(hdtSpec));
 			options.setTimeoutQuery(maxTimeoutCfg);
 			options.setTimeoutUpdate(maxTimeoutUpdateCfg);
 

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/compact/bitmap/MultiLayerBitmapWrapper.java

@@ -19,7 +19,7 @@ private MultiLayerModBitmapWrapper(ModifiableBitmap handle, long graphs) {
 
 		@Override
 		public void set(long layer, long position, boolean value) {
-			((ModifiableBitmap) handle).set(graphs * layer + position, value);
+			((ModifiableBitmap) handle).set(graphs * position + layer, value);
 		}
 	}
 
@@ -51,13 +51,14 @@ private MultiLayerBitmapWrapper(Bitmap handle, long graphs) {
 		this.graphs = graphs;
 	}
 
-	public Bitmap getHandle() {
-		return handle;
+	@SuppressWarnings("unchecked")
+	public <T extends Bitmap> T getHandle() {
+		return (T)handle;
 	}
 
 	@Override
 	public boolean access(long layer, long position) {
-		return handle.access(graphs * layer + position);
+		return handle.access(graphs * position + layer);
 	}
 
 	@Override
@@ -132,7 +133,7 @@ public long getLayersCount() {
 
 	@Override
 	public boolean access(long position) {
-		return handle.access(position);
+		return access(0, position);
 	}
 
 	@Override

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/iterator/utils/GraphFilteringTripleId.java

@@ -0,0 +1,103 @@
+package com.the_qa_company.qendpoint.core.iterator.utils;
+
+import com.the_qa_company.qendpoint.core.enums.ResultEstimationType;
+import com.the_qa_company.qendpoint.core.enums.TripleComponentOrder;
+import com.the_qa_company.qendpoint.core.exceptions.NotImplementedException;
+import com.the_qa_company.qendpoint.core.triples.IteratorTripleID;
+import com.the_qa_company.qendpoint.core.triples.TripleID;
+
+public class GraphFilteringTripleId implements IteratorTripleID {
+	private final IteratorTripleID iterator;
+	private final long[] graphIds;
+	private TripleID next;
+
+	public GraphFilteringTripleId(IteratorTripleID iterator, long[] graphIds) {
+		this.iterator = iterator;
+		this.graphIds = graphIds;
+	}
+
+	@Override
+	public boolean hasPrevious() {
+		throw new NotImplementedException();
+	}
+
+	@Override
+	public TripleID previous() {
+		throw new NotImplementedException();
+	}
+
+	@Override
+	public void goToStart() {
+		throw new NotImplementedException();
+	}
+
+	@Override
+	public boolean canGoTo() {
+		return false;
+	}
+
+	@Override
+	public void goTo(long pos) {
+		throw new NotImplementedException();
+	}
+
+	@Override
+	public long estimatedNumResults() {
+		return iterator.estimatedNumResults();
+	}
+
+	@Override
+	public ResultEstimationType numResultEstimation() {
+		return iterator.numResultEstimation();
+	}
+
+	@Override
+	public TripleComponentOrder getOrder() {
+		return iterator.getOrder();
+	}
+
+	@Override
+	public long getLastTriplePosition() {
+		return iterator.getLastTriplePosition();
+	}
+
+	@Override
+	public boolean isLastTriplePositionBoundToOrder() {
+		return iterator.isLastTriplePositionBoundToOrder();
+	}
+
+	@Override
+	public boolean hasNext() {
+		if (next != null) {
+			return true;
+		}
+		while (iterator.hasNext()) {
+			TripleID val = iterator.next();
+
+			long g = val.getGraph();
+			for (long graphId : graphIds) {
+				if (graphId == g) {
+					next = val;
+					return true;
+				}
+			}
+			// can't find valid graph
+		}
+		return false;
+	}
+
+	@Override
+	public TripleID next() {
+		if (!hasNext()) {
+			return null;
+		}
+		TripleID newVal = next;
+		next = null;
+		return newVal;
+	}
+
+	@Override
+	public void remove() {
+		throw new NotImplementedException();
+	}
+}

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/options/HDTOptions.java

@@ -30,7 +30,6 @@
 import java.io.Writer;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashSet;
@@ -92,7 +91,7 @@ static HDTOptions empty() {
 	 */
 	static HDTOptions of(HDTOptions other) {
 		HDTOptions opt = of();
-		other.getKeys().forEach(key -> opt.set(String.valueOf(key), other.get(String.valueOf(key))));
+		opt.setOptions(other);
 		return opt;
 	}
 
@@ -154,6 +153,18 @@ static HDTOptions of(Object... data) {
 		return opt;
 	}
 
+	/**
+	 * create modifiable options with a string config
+	 * @param cfg config
+	 * @return options
+	 */
+	static HDTOptions of(String cfg) {
+		Objects.requireNonNull(cfg, "cfg can't be null!");
+		HDTOptions opt = of();
+		opt.setOptions(cfg);
+		return opt;
+	}
+
 	/**
 	 * get options or {@link #EMPTY}
 	 *
@@ -248,13 +259,27 @@ default Path getPath(String key, Supplier<Path> defaultValue) {
 
 	/**
 	 * @return the keys of the options
-	 * @throws NotImplementedException if the implemented class do not implement
+	 * @throws NotImplementedException if the implementation does not implement
 	 *                                 this method (backward compatibility)
 	 */
 	default Set<?> getKeys() {
 		throw new NotImplementedException("getKeys");
 	}
 
+	/**
+	 * @return the options to be used with {@link #setOptions(String)}
+	 */
+	default String getOptions() {
+		StringBuilder bld = new StringBuilder();
+
+		for (Object k : getKeys()) {
+			String keyStr = String.valueOf(k);
+			bld.append(keyStr).append("=").append(get(keyStr)).append(";");
+		}
+
+		return bld.toString();
+	}
+
 	/**
 	 * get a value
 	 *
@@ -480,8 +505,7 @@ default void load(String filename) throws IOException {
 	void set(String key, String value);
 
 	/**
-	 * set a value, same as using {@link String#valueOf(Object)} with
-	 * {@link #set(String, String)}
+	 * set a value, check the type of the value to serialize it.
 	 *
 	 * @param key   key
 	 * @param value value
@@ -495,6 +519,11 @@ default void set(String key, Object value) {
 			set(key, p);
 		} else if (value instanceof File f) {
 			set(key, f.getAbsolutePath());
+		} else if (value instanceof HDTOptions opt) {
+			for (Object optKey : opt.getKeys()) {
+				String optKeyStr = String.valueOf(optKey);
+				set(key + "." + optKeyStr, opt.get(optKeyStr));
+			}
 		} else {
 			set(key, String.valueOf(value));
 		}
@@ -556,6 +585,14 @@ default void setOptions(Map<?, ?> options) {
 		options.forEach((k, v) -> set(String.valueOf(k), v));
 	}
 
+	/**
+	 * add options from another set
+	 * @param other other set
+	 */
+	default void setOptions(HDTOptions other) {
+		other.getKeys().forEach(key -> set(String.valueOf(key), other.get(String.valueOf(key))));
+	}
+
 	/**
 	 * add options, each param should be in the format (key, value)*
 	 *

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/quad/impl/BitmapTriplesIteratorGraph.java

@@ -49,6 +49,7 @@ protected TripleID getNext() {
 					return id;
 				}
 				// search another
+				tid = null;
 				continue;
 			}
 
@@ -105,6 +106,11 @@ public TripleComponentOrder getOrder() {
 		return tidIt.getOrder();
 	}
 
+	@Override
+	public boolean isLastTriplePositionBoundToOrder() {
+		return tidIt.isLastTriplePositionBoundToOrder();
+	}
+
 	@Override
 	public long getLastTriplePosition() {
 		return posZ;

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/triples/impl/BitmapQuadTriples.java

@@ -218,28 +218,6 @@ public void save(OutputStream output, ControlInfo ci, ProgressListener listener)
 		graphs.save(output, iListener);
 	}
 
-	@Override
-	public SuppliableIteratorTripleID search(TripleID pattern) {
-		if (isClosed) {
-			throw new IllegalStateException("Cannot search on BitmapTriples if it's already closed");
-		}
-
-		if (getNumberOfElements() == 0 || pattern.isNoMatch()) {
-			return new EmptyTriplesIterator(order);
-		}
-
-		TripleID reorderedPat = new TripleID(pattern);
-		TripleOrderConvert.swapComponentOrder(reorderedPat, TripleComponentOrder.SPO, order);
-		String patternString = reorderedPat.getPatternString();
-
-		if (hasFOQIndex() && patternString.equals("???G")) {
-			return new BitmapTriplesIteratorGraphG(this, pattern);
-		}
-
-		return new BitmapTriplesIteratorGraph(this, super.search(pattern.copyNoGraph()),
-				pattern.isQuad() ? pattern.getGraph() : 0);
-	}
-
 	@Override
 	public SuppliableIteratorTripleID search(TripleID pattern, int searchMask) {
 		if (isClosed) {

qendpoint-store/src/main/java/com/the_qa_company/qendpoint/compiler/CompiledSail.java

@@ -350,7 +350,7 @@ public static class CompiledSailCompiler {
 		private NotifyingSail sourceSail;
 		private EndpointFiles endpointFiles;
 		private HDTOptions spec;
-		private String hdtSpec;
+		private HDTOptions hdtSpec;
 		private final Map<String, String> stringConfig = new HashMap<>();
 		private final List<Object> stringObject = new ArrayList<>();
 		private CompiledSailOptions options;
@@ -518,6 +518,21 @@ public CompiledSailCompiler withEndpointFiles(EndpointFiles endpointFiles) {
 		 * @throws java.lang.NullPointerException a parameter is null
 		 */
 		public CompiledSailCompiler withHDTSpec(String hdtSpec) {
+			HDTOptions spec = HDTOptions.of();
+			spec.setOptions(hdtSpec);
+			return withHDTSpec(spec);
+		}
+
+
+		/**
+		 * set the hdt spec for the endpoint store, won't be used if the source
+		 * is defined or if the generated source isn't an endpoint store
+		 *
+		 * @param hdtSpec the spec
+		 * @return this
+		 * @throws java.lang.NullPointerException a parameter is null
+		 */
+		public CompiledSailCompiler withHDTSpec(HDTOptions hdtSpec) {
 			this.hdtSpec = Objects.requireNonNull(hdtSpec, "hdtSpec can't be null!");
 			return this;
 		}

qendpoint-store/src/main/java/com/the_qa_company/qendpoint/compiler/CompiledSailOptions.java

@@ -36,7 +36,7 @@ public class CompiledSailOptions {
 	private int rdf4jSplitUpdate;
 	private int endpointThreshold;
 	private int port;
-	private String hdtSpec;
+	private HDTOptions hdtSpec;
 	private int timeoutUpdate;
 	private int timeoutQuery;
 	private Map<String, String> hdtOptions;
@@ -74,7 +74,7 @@ public CompiledSailOptions() {
 		rdf4jSplitUpdate = SailCompilerSchema.RDF_STORE_SPLIT_STORAGE.getHandler().defaultValue();
 		endpointThreshold = SailCompilerSchema.ENDPOINT_THRESHOLD.getHandler().defaultValue();
 		port = SailCompilerSchema.SERVER_PORT.getHandler().defaultValue();
-		hdtSpec = "";
+		hdtSpec = HDTOptions.empty();
 		timeoutUpdate = SailCompilerSchema.TIMEOUT_UPDATE.getHandler().defaultValue();
 		timeoutQuery = SailCompilerSchema.TIMEOUT_QUERY.getHandler().defaultValue();
 		hdtOptions = Map.of();
@@ -96,7 +96,7 @@ void readOptions(SailCompiler.SailCompilerReader reader) {
 		endpointThreshold = reader.searchPropertyValue(SailCompilerSchema.MAIN, SailCompilerSchema.ENDPOINT_THRESHOLD);
 		hdtReadMode = reader.searchPropertyValue(SailCompilerSchema.MAIN, SailCompilerSchema.HDT_READ_MODE_PROPERTY);
 		port = reader.searchPropertyValue(SailCompilerSchema.MAIN, SailCompilerSchema.SERVER_PORT);
-		hdtSpec = reader.searchPropertyValue(SailCompilerSchema.MAIN, SailCompilerSchema.HDT_SPEC_PROPERTY);
+		hdtSpec = HDTOptions.of(reader.searchPropertyValue(SailCompilerSchema.MAIN, SailCompilerSchema.HDT_SPEC_PROPERTY));
 		timeoutUpdate = reader.searchPropertyValue(SailCompilerSchema.MAIN, SailCompilerSchema.TIMEOUT_UPDATE);
 		timeoutQuery = reader.searchPropertyValue(SailCompilerSchema.MAIN, SailCompilerSchema.TIMEOUT_QUERY);
 		hdtOptions = reader.search(SailCompilerSchema.MAIN, SailCompilerSchema.GEN_HDT_OPTION_PARAM).stream()
@@ -224,7 +224,7 @@ public void setPort(int port) {
 		this.port = port;
 	}
 
-	public String getHdtSpec() {
+	public HDTOptions getHdtSpec() {
 		return hdtSpec;
 	}
 
@@ -238,10 +238,7 @@ public void setDumpLocation(Path dumpLocation) {
 	 * @return HDTOptions
 	 */
 	public HDTOptions createSpecHDTOptions() {
-		HDTOptions opt = new HDTOptionsBase();
-
-		// set hdtspec config
-		opt.setOptions(getHdtSpec());
+		HDTOptions opt = HDTOptions.of(getHdtSpec());
 
 		// set model config
 		getHdtOptions().forEach(opt::set);
@@ -277,7 +274,7 @@ public HDTOptions createHDTOptions(Path endHDT, Path workLocation) {
 		return opt;
 	}
 
-	public void setHdtSpec(String hdtSpec) {
+	public void setHdtSpec(HDTOptions hdtSpec) {
 		this.hdtSpec = hdtSpec;
 	}