Some long overdue modularization but still not perfect; path finding,…

…tooling for concepts and the old shape code moved to separate modules
SmartDataAnalytics · Aug 11, 2020 · be84b1f · be84b1f
1 parent 09ff743
commit be84b1f
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diff --git a/dependency-notes.txt b/dependency-notes.txt
@@ -0,0 +1,24 @@
+rx
+	concepts
+	algebra
+	collections
+	provides SparqlRx and LookupApi (e.g. RangedSupplier; implemented in core)
+
+concepts
+	stmt
+
+stmt
+	utils
+
+
+algebra
+	utils
+	udf
+	concepts
+
+
+core
+	collections?
+	utils
+	concepts
+	rx
diff --git a/jena-sparql-api-algebra/pom.xml b/jena-sparql-api-algebra/pom.xml
@@ -1,47 +1,58 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-    <modelVersion>4.0.0</modelVersion>
-
-    <artifactId>jena-sparql-api-algebra</artifactId>
-    <packaging>jar</packaging>
-
-    <name>Jena SPARQL API - Algebra</name>
-
-    <parent>
-        <groupId>org.aksw.jena-sparql-api</groupId>
-        <artifactId>jena-sparql-api-parent</artifactId>
-        <version>3.15.0-1-SNAPSHOT</version>
-    </parent>
-
-    <dependencies>
-        <dependency>
-            <groupId>org.aksw.commons</groupId>
-            <artifactId>subgraph-isomorphism-index-jena</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>org.aksw.jena-sparql-api</groupId>
-            <artifactId>jena-sparql-api-utils</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>org.aksw.jena-sparql-api</groupId>
-            <artifactId>jena-sparql-api-udf</artifactId>
-        </dependency>
-
-
-        <!-- Unit Testing -->
-        <dependency>
-            <groupId>org.aksw.jena-sparql-api</groupId>
-            <artifactId>jena-sparql-api-resources-test-config</artifactId>
-            <scope>test</scope>
-        </dependency>
-
-        <!-- <dependency> -->
-        <!-- <groupId>org.slf4j</groupId> -->
-        <!-- <artifactId>slf4j-log4j12</artifactId> -->
-        <!-- </dependency> -->
-
-
-    </dependencies>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<artifactId>jena-sparql-api-algebra</artifactId>
+	<packaging>jar</packaging>
+
+	<name>Jena SPARQL API - Algebra</name>
+
+	<parent>
+		<groupId>org.aksw.jena-sparql-api</groupId>
+		<artifactId>jena-sparql-api-parent</artifactId>
+		<version>3.15.0-1-SNAPSHOT</version>
+	</parent>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.aksw.commons</groupId>
+			<artifactId>subgraph-isomorphism-index-jena</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.aksw.jena-sparql-api</groupId>
+			<artifactId>jena-sparql-api-utils</artifactId>
+		</dependency>
+
+<!-- 		<dependency> -->
+<!-- 			<groupId>org.aksw.jena-sparql-api</groupId> -->
+<!-- 			<artifactId>jena-sparql-api-concepts</artifactId> -->
+<!-- 		</dependency> -->
+
+		<dependency>
+			<groupId>org.aksw.jena-sparql-api</groupId>
+			<artifactId>jena-sparql-api-udf</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.aksw.jena-sparql-api</groupId>
+			<artifactId>jena-sparql-api-concepts</artifactId>
+		</dependency>
+
+		<!-- Unit Testing -->
+		<dependency>
+			<groupId>org.aksw.jena-sparql-api</groupId>
+			<artifactId>jena-sparql-api-resources-test-config</artifactId>
+			<scope>test</scope>
+		</dependency>
+
+		<!-- <dependency> -->
+		<!-- <groupId>org.slf4j</groupId> -->
+		<!-- <artifactId>slf4j-log4j12</artifactId> -->
+		<!-- </dependency> -->
+
+
+	</dependencies>
 </project>
diff --git a/...n/java/org/aksw/jena_sparql_api/algebra/expr/transform/ExprTransformVirtualBnodeUris.java b/...n/java/org/aksw/jena_sparql_api/algebra/expr/transform/ExprTransformVirtualBnodeUris.java
@@ -15,7 +15,7 @@
 import org.aksw.jena_sparql_api.algebra.transform.TransformPullFiltersIfCanMergeBGPs;
 import org.aksw.jena_sparql_api.algebra.transform.TransformReplaceConstants;
 import org.aksw.jena_sparql_api.algebra.utils.FixpointIteration;
-import org.aksw.jena_sparql_api.rx.SparqlStmtMgr;
+import org.aksw.jena_sparql_api.stmt.SparqlStmtMgr;
 import org.aksw.jena_sparql_api.user_defined_function.UserDefinedFunctions;
 import org.aksw.jena_sparql_api.utils.QueryUtils;
 import org.aksw.jena_sparql_api.utils.VarGeneratorBlacklist;

diff --git a/...i-algebra/src/main/java/org/aksw/jena_sparql_api/algebra/expr/transform/MainUdfTest2.java b/...i-algebra/src/main/java/org/aksw/jena_sparql_api/algebra/expr/transform/MainUdfTest2.java
@@ -6,7 +6,7 @@
 import java.util.Set;
 
 import org.aksw.jena_sparql_api.algebra.utils.FixpointIteration;
-import org.aksw.jena_sparql_api.rx.SparqlStmtMgr;
+import org.aksw.jena_sparql_api.stmt.SparqlStmtMgr;
 import org.aksw.jena_sparql_api.user_defined_function.UserDefinedFunctionResource;
 import org.aksw.jena_sparql_api.user_defined_function.UserDefinedFunctions;
 import org.aksw.jena_sparql_api.utils.Vars;

diff --git a/...core/utils/QueryGenerationUtilsTests.java → ...core/utils/QueryGenerationUtilsTests.java b/...core/utils/QueryGenerationUtilsTests.java → ...core/utils/QueryGenerationUtilsTests.java
@@ -7,6 +7,7 @@
 import java.util.Map.Entry;
 import java.util.function.Function;
 
+import org.aksw.jena_sparql_api.syntax.QueryGenerationUtils;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.sparql.core.Var;

diff --git a/jena-sparql-api-batch/pom.xml b/jena-sparql-api-batch/pom.xml
@@ -22,6 +22,11 @@
             <artifactId>jena-sparql-api-core</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>org.aksw.jena-sparql-api</groupId>
+            <artifactId>jena-sparql-api-resource-shape</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>org.aksw.jena-sparql-api</groupId>
             <artifactId>jena-sparql-api-mapper-core</artifactId>

diff --git a/...arql-api-batch/src/main/java/org/aksw/jena_sparql_api/batch/config/ConfigParsersCore.java b/...arql-api-batch/src/main/java/org/aksw/jena_sparql_api/batch/config/ConfigParsersCore.java
@@ -3,19 +3,19 @@
 import java.util.List;
 
 import org.aksw.jena_sparql_api.batch.cli.main.MainBatchWorkflow;
+import org.aksw.jena_sparql_api.concept.parser.SparqlConceptParser;
+import org.aksw.jena_sparql_api.concept.parser.SparqlConceptParserImpl;
+import org.aksw.jena_sparql_api.concept.parser.SparqlRelationParser;
+import org.aksw.jena_sparql_api.concept.parser.SparqlRelationParserImpl;
 import org.aksw.jena_sparql_api.shape.ResourceShapeParser;
 import org.aksw.jena_sparql_api.shape.ResourceShapeParserImpl;
 import org.aksw.jena_sparql_api.spring.conversion.ConverterRegistryPostProcessor;
-import org.aksw.jena_sparql_api.stmt.SparqlConceptParser;
-import org.aksw.jena_sparql_api.stmt.SparqlConceptParserImpl;
 import org.aksw.jena_sparql_api.stmt.SparqlElementParser;
 import org.aksw.jena_sparql_api.stmt.SparqlElementParserImpl;
 import org.aksw.jena_sparql_api.stmt.SparqlExprParser;
 import org.aksw.jena_sparql_api.stmt.SparqlExprParserImpl;
 import org.aksw.jena_sparql_api.stmt.SparqlQueryParser;
 import org.aksw.jena_sparql_api.stmt.SparqlQueryParserImpl;
-import org.aksw.jena_sparql_api.stmt.SparqlRelationParser;
-import org.aksw.jena_sparql_api.stmt.SparqlRelationParserImpl;
 import org.aksw.jena_sparql_api.stmt.SparqlUpdateParser;
 import org.aksw.jena_sparql_api.stmt.SparqlUpdateParserImpl;
 import org.springframework.beans.BeansException;

diff --git a/...api-batch/src/main/java/org/aksw/jena_sparql_api/spring/conversion/C_StringToConcept.java b/...api-batch/src/main/java/org/aksw/jena_sparql_api/spring/conversion/C_StringToConcept.java
@@ -1,7 +1,7 @@
 package org.aksw.jena_sparql_api.spring.conversion;
 
+import org.aksw.jena_sparql_api.concept.parser.SparqlConceptParser;
 import org.aksw.jena_sparql_api.concepts.Concept;
-import org.aksw.jena_sparql_api.stmt.SparqlConceptParser;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.convert.converter.Converter;
 

diff --git a/...pi-batch/src/main/java/org/aksw/jena_sparql_api/spring/conversion/C_StringToRelation.java b/...pi-batch/src/main/java/org/aksw/jena_sparql_api/spring/conversion/C_StringToRelation.java
@@ -1,7 +1,7 @@
 package org.aksw.jena_sparql_api.spring.conversion;
 
+import org.aksw.jena_sparql_api.concept.parser.SparqlRelationParser;
 import org.aksw.jena_sparql_api.concepts.BinaryRelation;
-import org.aksw.jena_sparql_api.stmt.SparqlRelationParser;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.convert.converter.Converter;
 

diff --git a/jena-sparql-api-batch/src/test/java/org/aksw/jena_sparql_api/batch/TestParsers.java b/jena-sparql-api-batch/src/test/java/org/aksw/jena_sparql_api/batch/TestParsers.java
@@ -1,10 +1,10 @@
 package org.aksw.jena_sparql_api.batch;
 
+import org.aksw.jena_sparql_api.concept.parser.SparqlRelationParser;
+import org.aksw.jena_sparql_api.concept.parser.SparqlRelationParserImpl;
 import org.aksw.jena_sparql_api.concepts.BinaryRelation;
 import org.aksw.jena_sparql_api.stmt.SparqlElementParserImpl;
 import org.aksw.jena_sparql_api.stmt.SparqlQueryParserImpl;
-import org.aksw.jena_sparql_api.stmt.SparqlRelationParser;
-import org.aksw.jena_sparql_api.stmt.SparqlRelationParserImpl;
 import org.junit.Test;
 
 import org.apache.jena.query.Syntax;

diff --git a/jena-sparql-api-cache-h2/src/main/java/org/aksw/jena_sparql_api/cache/h2/CacheCoreH2.java b/jena-sparql-api-cache-h2/src/main/java/org/aksw/jena_sparql_api/cache/h2/CacheCoreH2.java
@@ -19,9 +19,7 @@
 import org.aksw.jena_sparql_api.cache.extra.CacheCore;
 import org.aksw.jena_sparql_api.cache.extra.CacheCoreExCompressor;
 import org.aksw.jena_sparql_api.cache.extra.CacheEntry;
-import org.aksw.jena_sparql_api.cache.extra.CacheEntryBase;
 import org.aksw.jena_sparql_api.cache.extra.CacheEntryImpl;
-import org.aksw.jena_sparql_api.cache.extra.InputStreamProviderResultSetBlob;
 import org.aksw.jena_sparql_api.cache.extra.SqlDaoBase;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -46,7 +44,7 @@ public class CacheCoreH2
     private static final Logger logger = LoggerFactory.getLogger(CacheCoreH2.class);
 
     private boolean validateHash = true;
-    
+
     private String defaultService = "";
 
     @Override
@@ -76,15 +74,15 @@ enum Query
     }
 
 
-	private String databaseDirectory = "cache";
-	private String databaseName = "extraction";
-	private boolean autoServerMode = true;
+    private String databaseDirectory = "cache";
+    private String databaseName = "extraction";
+    private boolean autoServerMode = true;
 
-	// specifies after how many milli seconds a cached result becomes invalid
-	private long lifespan = 1 * 24 * 60 * 60 * 1000; // 1 day
+    // specifies after how many milli seconds a cached result becomes invalid
+    private long lifespan = 1 * 24 * 60 * 60 * 1000; // 1 day
 
 
-	private Connection conn;
+    private Connection conn;
 
 
     public static CacheCoreH2 create(String dbName)
@@ -136,8 +134,8 @@ public static CacheBackend create(String dbName, long lifespan, boolean useCompr
         return create(true, "cache/sparql", dbName, lifespan, useCompression);
     }
 
-    
-	public CacheCoreH2(Connection conn, long lifespan)
+
+    public CacheCoreH2(Connection conn, long lifespan)
             throws SQLException
     {
         super(Arrays.asList(Query.values()));
@@ -288,10 +286,10 @@ public String createHashRoot(String service, String queryString) {
         return service + queryString;
     }
 
-	@Override
-	public boolean isReadOnly() {
-		// TODO Auto-generated method stub
-		return false;
-	}
+    @Override
+    public boolean isReadOnly() {
+        // TODO Auto-generated method stub
+        return false;
+    }
 
 }
diff --git a/...c/main/java/org/aksw/jena_sparql_api/concept_cache/core/OpRewriteViewMatcherStateful.java b/...c/main/java/org/aksw/jena_sparql_api/concept_cache/core/OpRewriteViewMatcherStateful.java
@@ -26,9 +26,9 @@
 import org.aksw.jena_sparql_api.concept_cache.dirty.QfpcMatch;
 import org.aksw.jena_sparql_api.concept_cache.dirty.SparqlViewMatcherQfpcImpl;
 import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplier;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplierLazyLoadingListCache;
 import org.aksw.jena_sparql_api.util.collection.CacheRangeInfo;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplier;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplierLazyLoadingListCache;
 import org.aksw.jena_sparql_api.utils.ResultSetUtils;
 import org.aksw.jena_sparql_api.view_matcher.OpVarMap;
 import org.aksw.jena_sparql_api.views.index.SparqlViewMatcherOpImpl;

diff --git a/...in/java/org/aksw/jena_sparql_api/concept_cache/core/QueryExecutionFactoryLazyLoading.java b/...in/java/org/aksw/jena_sparql_api/concept_cache/core/QueryExecutionFactoryLazyLoading.java
@@ -4,7 +4,7 @@
 
 import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
 import org.aksw.jena_sparql_api.core.QueryExecutionFactoryDecorator;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplier;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplier;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.sparql.engine.binding.Binding;

diff --git a/.../src/main/java/org/aksw/jena_sparql_api/concept_cache/core/QueryExecutionLazyLoading.java b/.../src/main/java/org/aksw/jena_sparql_api/concept_cache/core/QueryExecutionLazyLoading.java
@@ -4,7 +4,7 @@
 import java.util.stream.Stream;
 
 import org.aksw.jena_sparql_api.core.ResultSetCloseable;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplierLazyLoadingListCache;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplierLazyLoadingListCache;
 import org.aksw.jena_sparql_api.utils.ResultSetUtils;
 import org.apache.jena.query.ResultSet;
 import org.apache.jena.sparql.engine.binding.Binding;

diff --git a/...ain/java/org/aksw/jena_sparql_api/concept_cache/core/QueryExecutionViewMatcherMaster.java b/...ain/java/org/aksw/jena_sparql_api/concept_cache/core/QueryExecutionViewMatcherMaster.java
@@ -22,8 +22,8 @@
 import org.aksw.jena_sparql_api.core.QueryExecutionBaseSelect;
 import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
 import org.aksw.jena_sparql_api.core.ResultSetCloseable;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplier;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplierLazyLoadingListCache;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplier;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplierLazyLoadingListCache;
 import org.aksw.jena_sparql_api.utils.BindingUtils;
 import org.aksw.jena_sparql_api.utils.QueryUtils;
 import org.aksw.jena_sparql_api.utils.ResultSetUtils;

diff --git a/...api-cache/src/main/java/org/aksw/jena_sparql_api/concept_cache/core/RangedSupplierOp.java b/...api-cache/src/main/java/org/aksw/jena_sparql_api/concept_cache/core/RangedSupplierOp.java
@@ -1,8 +1,8 @@
 package org.aksw.jena_sparql_api.concept_cache.core;
 
 import org.aksw.jena_sparql_api.algebra.transform.TransformPushSlice;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplier;
 import org.aksw.jena_sparql_api.util.RewriteUtils;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplier;
 import org.aksw.jena_sparql_api.utils.QueryUtils;
 import org.apache.jena.sparql.algebra.Op;
 import org.apache.jena.sparql.algebra.Transformer;

diff --git a/...-cache/src/main/java/org/aksw/jena_sparql_api/concept_cache/core/RangedSupplierQuery.java b/...-cache/src/main/java/org/aksw/jena_sparql_api/concept_cache/core/RangedSupplierQuery.java
@@ -2,7 +2,7 @@
 
 import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
 import org.aksw.jena_sparql_api.rx.SparqlRx;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplier;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplier;
 import org.aksw.jena_sparql_api.utils.QueryUtils;
 import org.apache.jena.query.Query;
 import org.apache.jena.sparql.algebra.Algebra;

diff --git a/...rql-api-cache/src/main/java/org/aksw/jena_sparql_api/concept_cache/core/StorageEntry.java b/...rql-api-cache/src/main/java/org/aksw/jena_sparql_api/concept_cache/core/StorageEntry.java
@@ -1,7 +1,7 @@
 package org.aksw.jena_sparql_api.concept_cache.core;
 
 import org.aksw.jena_sparql_api.algebra.analysis.VarInfo;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplier;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplier;
 import org.apache.jena.sparql.engine.binding.Binding;
 
 public class StorageEntry {

diff --git a/...ql-api-cache/src/test/java/org/aksw/jena_sparql_api/cache/tests/TestStateSpaceSearch.java b/...ql-api-cache/src/test/java/org/aksw/jena_sparql_api/cache/tests/TestStateSpaceSearch.java
@@ -44,13 +44,13 @@
 import org.aksw.jena_sparql_api.core.FluentQueryExecutionFactory;
 import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
 import org.aksw.jena_sparql_api.parse.QueryExecutionFactoryParse;
+import org.aksw.jena_sparql_api.rx.util.collection.RangedSupplier;
 import org.aksw.jena_sparql_api.sparql.algebra.mapping.SequentialMatchIterator;
 import org.aksw.jena_sparql_api.sparql.algebra.mapping.VarMapper;
 import org.aksw.jena_sparql_api.stmt.SparqlElementParser;
 import org.aksw.jena_sparql_api.stmt.SparqlElementParserImpl;
 import org.aksw.jena_sparql_api.stmt.SparqlQueryParserImpl;
 import org.aksw.jena_sparql_api.unsorted.ExprMatcher;
-import org.aksw.jena_sparql_api.util.collection.RangedSupplier;
 import org.aksw.jena_sparql_api.utils.DnfUtils;
 import org.aksw.jena_sparql_api.utils.VarGeneratorImpl2;
 import org.aksw.jena_sparql_api.view_matcher.OpVarMap;