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Updated build to latest changes in dependencies
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Aklakan committed Oct 24, 2023
1 parent ac3947f commit ef37e29
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Showing 24 changed files with 56 additions and 56 deletions.
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Expand Up @@ -32,4 +32,4 @@ public Integer call() throws Exception {
return 0;
}

}
}
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Expand Up @@ -46,9 +46,9 @@ public Integer call() throws Exception {
Resource r = ds.getModel().createResource(ds.getGraphName());
// System.err.println("Starting processing: " + r);

if (r.toString().contains("3B0r_bVVjj377f2RT0CXPK-XvLFN4CVMaPXrc6leOCw")) {
System.out.println("here");
}
// if (r.toString().contains("3B0r_bVVjj377f2RT0CXPK-XvLFN4CVMaPXrc6leOCw")) {
// System.out.println("here");
// }

Resource skolemized = enricher.apply(r);

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Expand Up @@ -35,11 +35,11 @@
import org.aksw.jena_sparql_api.rx.dataset.DatasetFlowOps;
import org.aksw.jena_sparql_api.rx.dataset.ResourceInDatasetFlowOps;
import org.aksw.jena_sparql_api.rx.script.SparqlScriptProcessor;
import org.aksw.jenax.arq.connection.core.SparqlQueryConnectionWithReconnect;
import org.aksw.jenax.arq.dataset.api.ResourceInDataset;
import org.aksw.jenax.arq.dataset.impl.ResourceInDatasetImpl;
import org.aksw.jenax.arq.dataset.orderaware.DatasetFactoryEx;
import org.aksw.jenax.arq.dataset.orderaware.DatasetGraphFactoryEx;
import org.aksw.jenax.dataaccess.sparql.connection.reconnect.SparqlQueryConnectionWithReconnect;
import org.aksw.jenax.reprogen.core.MapperProxyUtils;
import org.aksw.jenax.reprogen.hashid.HashIdCxt;
import org.aksw.jenax.sparql.query.rx.RDFDataMgrRx;
Expand Down Expand Up @@ -69,7 +69,6 @@
import org.aksw.simba.lsq.vocab.PROV;
import org.apache.commons.io.output.CloseShieldOutputStream;
import org.apache.jena.datatypes.xsd.XSDDateTime;
import org.apache.jena.ext.com.google.common.hash.Hashing;
import org.apache.jena.query.Dataset;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Property;
Expand All @@ -94,6 +93,7 @@
import org.slf4j.LoggerFactory;
import org.spinrdf.vocabulary.SP;

import com.google.common.hash.Hashing;
import com.google.common.io.BaseEncoding;

import io.reactivex.rxjava3.core.Flowable;
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Expand Up @@ -15,7 +15,7 @@
import org.aksw.simba.lsq.model.RemoteExecution;
import org.aksw.simba.lsq.parser.WebLogParser;
import org.aksw.simba.lsq.vocab.LSQ;
import org.apache.jena.ext.com.google.common.collect.Iterables;
import com.google.common.collect.Iterables;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.riot.RDFDataMgr;
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Expand Up @@ -13,7 +13,7 @@
import org.aksw.simba.lsq.core.ResourceParser;
import org.aksw.simba.lsq.core.io.input.registry.LsqInputFormatRegistry;
import org.aksw.simba.lsq.vocab.LSQ;
import org.apache.jena.ext.com.google.common.collect.Maps;
import com.google.common.collect.Maps;
import org.apache.jena.rdf.model.Resource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
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Expand Up @@ -28,8 +28,8 @@
import org.aksw.simba.lsq.parser.Mapper;
import org.aksw.simba.lsq.vocab.LSQ;
import org.apache.commons.io.IOUtils;
import org.apache.jena.ext.com.google.common.base.Strings;
import org.apache.jena.ext.com.google.common.collect.Maps;
import com.google.common.base.Strings;
import com.google.common.collect.Maps;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Resource;
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Expand Up @@ -19,7 +19,7 @@
import org.aksw.jenax.arq.util.var.Vars;
import org.aksw.jenax.reprogen.core.MapperProxyUtils;
import org.aksw.jenax.reprogen.hashid.HashIdCxt;
import org.apache.jena.ext.com.google.common.hash.HashCode;
import com.google.common.hash.HashCode;
import org.apache.jena.graph.Graph;
import org.apache.jena.graph.Node;
import org.apache.jena.graph.NodeFactory;
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@@ -1,9 +1,8 @@
package org.aksw.simba.lsq.util;

import org.aksw.jena_sparql_api.concepts.Concept;
import org.aksw.jena_sparql_api.concepts.ConceptUtils;
import org.aksw.jenax.sparql.fragment.api.Fragment1;
import org.aksw.jenax.sparql.fragment.impl.ConceptUtils;
import org.aksw.jenax.sparql.query.rx.SparqlRx;
import org.aksw.jenax.sparql.relation.api.UnaryRelation;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.rdf.model.Model;
Expand All @@ -14,7 +13,7 @@
import io.reactivex.rxjava3.core.Flowable;

public class ConceptModelUtils {
public static <T extends Resource> Flowable<T> listResources(Model model, Concept concept, Class<? extends T> clazz) {
public static <T extends Resource> Flowable<T> listResources(Model model, Fragment1 concept, Class<? extends T> clazz) {
return listRdfNodes(model, concept)
// .filter(rdfNode -> rdfNode.canAs(clazz))
.filter(rdfNode -> {
Expand Down Expand Up @@ -43,7 +42,7 @@ public static <T extends Resource> Flowable<T> listResources(Model model, Concep
*/
public static <T extends Resource> Flowable<T> listResourcesUnchecked(
Model model,
UnaryRelation concept,
Fragment1 concept,
Class<? extends T> clazz) {
return listRdfNodes(model, concept)
.map(rdfNode -> {
Expand All @@ -63,7 +62,7 @@ public static <T extends Resource> Flowable<T> listResourcesUnchecked(
// return result;
// }

public static Flowable<RDFNode> listRdfNodes(Model model, UnaryRelation concept) {
public static Flowable<RDFNode> listRdfNodes(Model model, Fragment1 concept) {
Var var = concept.getVar();
Query query = ConceptUtils.createQueryList(concept);

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Expand Up @@ -4,7 +4,7 @@

import org.aksw.simba.lsq.util.ElementVisitorFeatureExtractor;
import org.aksw.simba.lsq.vocab.LSQ;
import org.apache.jena.ext.com.google.common.collect.ImmutableMap;
import com.google.common.collect.ImmutableMap;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.rdf.model.Resource;
import org.junit.Assert;
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Expand Up @@ -14,8 +14,8 @@
import org.aksw.simba.lsq.parser.WebLogParser;
import org.aksw.simba.lsq.vocab.LSQ;
import org.aksw.simba.lsq.vocab.PROV;
import org.apache.jena.ext.com.google.common.reflect.ClassPath;
import org.apache.jena.ext.com.google.common.reflect.ClassPath.ResourceInfo;
import com.google.common.reflect.ClassPath;
import com.google.common.reflect.ClassPath.ResourceInfo;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.riot.RDFDataMgr;
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Expand Up @@ -26,18 +26,18 @@

import org.aksw.commons.io.util.StdIo;
import org.aksw.jena_sparql_api.rx.query_flow.QueryFlowOps;
import org.aksw.jenax.arq.connection.core.ConnectionLostException;
import org.aksw.jenax.arq.dataset.api.ResourceInDataset;
import org.aksw.jenax.arq.dataset.impl.ResourceInDatasetImpl;
import org.aksw.jenax.arq.util.binding.ResultSetUtils;
import org.aksw.jenax.arq.util.exec.QueryExecutionUtils;
import org.aksw.jenax.arq.util.exec.query.QueryExecutionUtils;
import org.aksw.jenax.arq.util.expr.ExprUtils;
import org.aksw.jenax.arq.util.quad.DatasetUtils;
import org.aksw.jenax.arq.util.quad.Quads;
import org.aksw.jenax.arq.util.syntax.ElementUtils;
import org.aksw.jenax.arq.util.syntax.QueryGenerationUtils;
import org.aksw.jenax.arq.util.update.UpdateRequestUtils;
import org.aksw.jenax.arq.util.var.Vars;
import org.aksw.jenax.dataaccess.sparql.connection.reconnect.ConnectionLostException;
import org.aksw.jenax.reprogen.core.MapperProxyUtils;
import org.aksw.jenax.reprogen.hashid.HashIdCxt;
import org.aksw.jenax.sparql.query.rx.RDFDataMgrRx;
Expand All @@ -57,7 +57,6 @@
import org.aksw.simba.lsq.vocab.LSQ;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.jena.datatypes.xsd.XSDDateTime;
import org.apache.jena.ext.com.google.common.base.Stopwatch;
import org.apache.jena.graph.Node;
import org.apache.jena.graph.NodeFactory;
import org.apache.jena.query.Dataset;
Expand Down Expand Up @@ -92,6 +91,8 @@
import org.slf4j.LoggerFactory;
import org.spinrdf.model.TriplePattern;

import com.google.common.base.Stopwatch;

import io.reactivex.rxjava3.core.Flowable;
import io.reactivex.rxjava3.core.FlowableTransformer;
import io.reactivex.rxjava3.core.Maybe;
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Expand Up @@ -17,13 +17,13 @@

import org.aksw.commons.collections.MapUtils;
import org.aksw.commons.util.string.StringUtils;
import org.aksw.jena_sparql_api.concepts.Concept;
import org.aksw.jena_sparql_api.concepts.ConceptUtils;
import org.aksw.jenax.arq.connection.core.QueryExecutionFactory;
import org.aksw.jenax.arq.util.exec.QueryExecutionUtils;
import org.aksw.jenax.arq.util.exec.query.QueryExecutionUtils;
import org.aksw.jenax.arq.util.syntax.ElementUtils;
import org.aksw.jenax.arq.util.triple.TripleUtils;
import org.aksw.jenax.arq.util.var.Vars;
import org.aksw.jenax.dataaccess.sparql.factory.execution.query.QueryExecutionFactory;
import org.aksw.jenax.sparql.fragment.impl.Concept;
import org.aksw.jenax.sparql.fragment.impl.ConceptUtils;
import org.aksw.simba.lsq.model.util.SpinCoreUtils;
import org.aksw.simba.lsq.spinx.model.Bgp;
import org.aksw.simba.lsq.spinx.model.SpinQueryEx;
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Expand Up @@ -4,8 +4,8 @@
import java.util.Set;
import java.util.stream.Collectors;

import org.aksw.jena_sparql_api.concepts.Concept;
import org.aksw.jenax.sparql.relation.api.UnaryRelation;
import org.aksw.jenax.sparql.fragment.api.Fragment1;
import org.aksw.jenax.sparql.fragment.impl.Concept;
import org.aksw.simba.lsq.util.ConceptModelUtils;
import org.apache.jena.graph.Node;
import org.apache.jena.rdf.model.Model;
Expand All @@ -23,7 +23,7 @@
/** Utils for accessing certain information in a spin model */
public class SpinAccessUtils {

public static final UnaryRelation tpListStarts = Concept.create(
public static final Fragment1 tpListStarts = Concept.create(
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>"
+ "PREFIX sp: <http://spinrdf.org/sp#>",
"listStart",
Expand All @@ -34,7 +34,7 @@ public class SpinAccessUtils {
);


public static final UnaryRelation tpNoList = Concept.create(
public static final Fragment1 tpNoList = Concept.create(
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>"
+ "PREFIX sp: <http://spinrdf.org/sp#>",
"listStart",
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Expand Up @@ -17,8 +17,8 @@
import org.aksw.simba.lsq.core.LsqUtils;
import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
import org.apache.jena.atlas.iterator.Iter;
import org.apache.jena.ext.com.google.common.base.Stopwatch;
import org.apache.jena.ext.com.google.common.collect.Iterators;
import com.google.common.base.Stopwatch;
import com.google.common.collect.Iterators;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
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Expand Up @@ -39,8 +39,8 @@
import org.aksw.simba.lsq.vocab.PROV;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.jena.datatypes.xsd.XSDDateTime;
import org.apache.jena.ext.com.google.common.base.Stopwatch;
import org.apache.jena.ext.com.google.common.hash.Hashing;
import com.google.common.base.Stopwatch;
import com.google.common.hash.Hashing;
import org.apache.jena.graph.Node;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
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Expand Up @@ -7,7 +7,7 @@
import org.aksw.commons.rx.op.FlowableOperatorSequentialGroupBy;
import org.aksw.jena_sparql_api.rx.RDFDataMgrRx;
import org.aksw.simba.lsq.model.LsqQuery;
import org.apache.jena.ext.com.google.common.collect.Maps;
import com.google.common.collect.Maps;
import org.apache.jena.riot.Lang;

import io.reactivex.rxjava3.core.Flowable;
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Expand Up @@ -9,7 +9,7 @@
import java.util.Collections;
import java.util.Map.Entry;

import org.apache.jena.ext.com.google.common.primitives.Ints;
import com.google.common.primitives.Ints;

import com.google.common.collect.ImmutableMap;
import com.google.common.hash.HashCode;
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Expand Up @@ -9,9 +9,9 @@
import org.aksw.jenax.annotation.reprogen.Iri;
import org.aksw.jenax.annotation.reprogen.ResourceView;
import org.aksw.simba.lsq.vocab.LSQ;
import org.apache.jena.ext.com.google.common.hash.HashCode;
import org.apache.jena.ext.com.google.common.hash.Hashing;
import org.apache.jena.ext.com.google.common.io.BaseEncoding;
import com.google.common.hash.HashCode;
import com.google.common.hash.Hashing;
import com.google.common.io.BaseEncoding;
import org.apache.jena.query.Query;
import org.apache.jena.rdf.model.Resource;

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Expand Up @@ -3,7 +3,7 @@
import java.util.regex.Pattern;

import org.apache.jena.datatypes.RDFDatatype;
import org.apache.jena.ext.com.google.common.base.Converter;
import com.google.common.base.Converter;

public class FieldSpec {

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Expand Up @@ -96,7 +96,7 @@ public static Map<String, SourceOfRddOfResources> loadCsvRegistry(JavaSparkConte

public static SourceOfRddOfResources createCsvSource(JavaSparkContext sc, String queryStr) {
// CSVFormat csvFormat = CSVFormat.Builder.create(CSVFormat.EXCEL).setSkipHeaderRecord(true).build();
UnivocityCsvwConf csvConf = new UnivocityCsvwConf(new DialectMutableImpl().setHeader(true));
UnivocityCsvwConf csvConf = new UnivocityCsvwConf(new DialectMutableImpl().setHeader(true), null);

return source -> {
Query query = QueryFactory.create(queryStr);
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Expand Up @@ -6,8 +6,8 @@
import java.util.function.Function;
import java.util.function.Supplier;

import org.aksw.commons.util.stream.SequentialGroupBySpec;
import org.aksw.commons.util.stream.StreamOperatorSequentialGroupBy;
import org.aksw.commons.util.stream.CollapseRunsSpec;
import org.aksw.commons.util.stream.StreamOperatorCollapseRuns;
import org.apache.jena.graph.Node;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.DatasetFactory;
Expand All @@ -17,7 +17,7 @@
public class DatasetGraphOpsStream {
public static StreamTransformer<Quad, Entry<Node, List<Quad>>> groupToList()
{
return StreamOperatorSequentialGroupBy.<Quad, Node, List<Quad>>create(SequentialGroupBySpec.create(
return StreamOperatorCollapseRuns.<Quad, Node, List<Quad>>create(CollapseRunsSpec.create(
Quad::getGraph,
graph -> new ArrayList<>(),
(list, item) -> list.add(item)
Expand All @@ -28,7 +28,7 @@ public static StreamTransformer<Quad, Entry<Node, DatasetGraph>> groupConsecutiv
Function<Quad, Node> grouper,
Supplier<? extends DatasetGraph> graphSupplier) {

return StreamOperatorSequentialGroupBy.<Quad, Node, DatasetGraph>create(SequentialGroupBySpec.create(
return StreamOperatorCollapseRuns.<Quad, Node, DatasetGraph>create(CollapseRunsSpec.create(
grouper::apply,
groupKey -> graphSupplier.get(),
DatasetGraph::add))::transform;
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Expand Up @@ -4,8 +4,8 @@
import java.util.function.Function;
import java.util.function.Supplier;

import org.aksw.commons.util.stream.SequentialGroupBySpec;
import org.aksw.commons.util.stream.StreamOperatorSequentialGroupBy;
import org.aksw.commons.util.stream.CollapseRunsSpec;
import org.aksw.commons.util.stream.StreamOperatorCollapseRuns;
import org.apache.jena.graph.Graph;
import org.apache.jena.graph.Node;
import org.apache.jena.graph.Triple;
Expand All @@ -16,7 +16,7 @@ public static StreamTransformer<Triple, Entry<Node, Graph>> groupConsecutiveTrip
Function<Triple, Node> grouper,
Supplier<Graph> graphSupplier) {

return StreamOperatorSequentialGroupBy.<Triple, Node, Graph>create(SequentialGroupBySpec.create(
return StreamOperatorCollapseRuns.<Triple, Node, Graph>create(CollapseRunsSpec.create(
grouper::apply,
groupKey -> graphSupplier.get(),
Graph::add))::transform;
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Expand Up @@ -6,7 +6,7 @@
import org.aksw.commons.model.csvw.domain.impl.DialectMutableImpl;
import org.aksw.commons.model.csvw.univocity.UnivocityCsvwConf;
import org.aksw.jenax.arq.picocli.CmdMixinArq;
import org.aksw.jenax.arq.util.exec.ExecutionContextUtils;
import org.aksw.jenax.arq.util.exec.query.ExecutionContextUtils;
import org.aksw.jenax.arq.util.security.ArqSecurity;
import org.apache.jena.query.ARQ;
import org.apache.jena.query.Query;
Expand Down Expand Up @@ -81,7 +81,7 @@ public static void main(String[] args) throws Exception {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(ss.sparkContext());

// CSVFormat baseCsvFormat = CSVFormat.Builder.create(CSVFormat.EXCEL).setSkipHeaderRecord(true).build();
UnivocityCsvwConf csvConf = new UnivocityCsvwConf(new DialectMutableImpl().setHeader(true));
UnivocityCsvwConf csvConf = new UnivocityCsvwConf(new DialectMutableImpl().setHeader(true), null);


String path = "/home/raven/Datasets/bio2rdf_sparql_logs_processed_01-2019_to_07-2021.csv";
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10 changes: 5 additions & 5 deletions pom.xml
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Expand Up @@ -63,12 +63,12 @@
</modules>

<properties>
<jena.version>4.8.0</jena.version>
<jenax.version>4.8.0-2</jenax.version>
<aksw-commons.version>0.9.6</aksw-commons.version>
<sansa.version>0.8.7</sansa.version>
<jena.version>4.9.0</jena.version>
<jenax.version>4.9.0-1-SNAPSHOT</jenax.version>
<aksw-commons.version>0.9.7-SNAPSHOT</aksw-commons.version>
<sansa.version>0.9.0-SNAPSHOT</sansa.version>

<spark.version>3.0.1</spark.version>
<spark.version>3.3.2</spark.version>
<spark.deps.scope>compile</spark.deps.scope>

<scala.binary.version>2.12</scala.binary.version>
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