Updates for revised SPARQL APIs

.gitignore

@@ -9,3 +9,6 @@ target/
 *.iml
 .idea
 .java-version
+
+# Hugo
+.hugo_build.lock

source/documentation/query/http-auth.md → source/documentation/archive/versions/http-auth-old.md

@@ -1,5 +1,9 @@
 ---
-title: HTTP Authentication in ARQ
+title: HTTP Authentication in ARQ (Superseded)
+---
+
+<i>Documentation for HTTP Authentication (Jena3.1.1 to Jena 4.2.0) using Apache Commons HttpClient.</i>
+
 ---
 
 After [Jena 3.1.0](#http-authentication-from-jena-311), Jena exposes the underlying HTTP Commons functionality to support a range of authentication mechanisms as well as [other HTTP configuration][16]. From [Jena 3.0.0 through Jena 3.1.0](#http-authentication-from-jena-300-through-310) there is a Jena-specific framework that provides a uniform mechanism for HTTP authentication. This documentation is therefore divided into two sections. The first explains how to use HTTP Commons code, and the second explains the older Jena-specific functionality.

source/documentation/fuseki2/fuseki-embedded.md

@@ -34,7 +34,7 @@ or read the dataset and see any updates made by remote systems:
     // Read transaction.
     Txn.execRead(dsg, ()->{
     Dataset ds = DatasetFactory.wrap(dsg) ;
-    try (QueryExecution qExec = QueryExecutionFactory.create("SELECT * { ?s  ?o}", ds) ) {
+    try (QueryExecution qExec = QueryExecution.create("SELECT * { ?s  ?o}", ds) ) {
         ResultSet rs = qExec.execSelect() ;
         ResultSetFormatter.out(rs) ;
       }

source/documentation/fuseki2/fuseki-main-security.md

@@ -0,0 +1,13 @@
+---
+title: Security in Fuseki2 server
+---
+This page covers security for Fuseki Main.
+
+See other [documentation](./fusek0-security.html) for the webapp packaging of Fuseki.
+
+## Serving RDF
+
+For any use of users-password information, and especially HTTP basic
+authentication, information is visible in the HTTP headers. When serving RDF and SPARQL requests, using HTTPS is necessary to avoid snooping.
+Digest authentication is also stronger over HTTPS
+because it protects against man-in-the-middle attacks.

source/documentation/geosparql/__index.md

@@ -107,7 +107,7 @@ To query a Model with GeoSPARQL or standard SPARQL:
     Model model = .....;
     String query = ....;
 
-    try (QueryExecution qe = QueryExecutionFactory.create(query, model)) {
+    try (QueryExecution qe = QueryExecution.create(query, model)) {
         ResultSet rs = qe.execSelect();
         ResultSetFormatter.outputAsTSV(rs);
     }

source/documentation/geosparql/geosparql-fuseki.md

@@ -94,7 +94,7 @@ Once the default server is running it can be queried using Jena as follows:
 
     String service = "http://localhost:3030/ds";
     String query = ....;
-    try (QueryExecution qe = QueryExecutionFactory.sparqlService(service, query)) {
+    try (QueryExecution qe = QueryExecution.service(service).query(query).build()) {
         ResultSet rs = qe.execSelect();
         ResultSetFormatter.outputAsTSV(rs);
     }

source/documentation/query/__index.md

@@ -11,80 +11,80 @@ SPARQL is the query language developed by the W3C
 
 ## ARQ Features
 
--   Standard SPARQL
--   Free text search via Lucene
--   SPARQL/Update
--   Access and extension of the SPARQL algebra
--   Support for custom filter functions, including javascript functions
--   Property functions for custom processing of semantic
+- Standard SPARQL
+- Free text search via Lucene
+- SPARQL/Update
+- Access and extension of the SPARQL algebra
+- Support for custom filter functions, including javascript functions
+- Property functions for custom processing of semantic
     relationships
--   Aggregation, GROUP BY and assignment as SPARQL extensions
--   Support for federated query
--   Support for extension to other storage systems
--   Client-support for remote access to any SPARQL endpoint
+- Aggregation, GROUP BY and assignment as SPARQL extensions
+- Support for federated query
+- Support for extension to other storage systems
+- Client-support for remote access to any SPARQL endpoint
 
 ## Introduction
 
--   [A Brief Tutorial on SPARQL](/tutorials/sparql.html)
--   [Application API](app_api.html) - covers the majority of
+- [A Brief Tutorial on SPARQL](/tutorials/sparql.html)
+- [Application API](app_api.html) - covers the majority of
     application usages
--   [Frequently Asked Questions](faq.html)
--   [ARQ Support](support.html)
--   Application [javadoc](/documentation/javadoc/arq/index.html)
--   [Command line utilities](cmds.html)
--   [Querying remote SPARQL services](sparql-remote.html)
-    - [HTTP Authentication for ARQ](http-auth.html)
--   [Logging](logging.html)
--   [Explaining queries](explain.html)
--   [Tutorial: manipulating SPARQL using ARQ](manipulating_sparql_using_arq.html)
--   [Basic federated query (`SERVICE`)](service.html)
--   [Property paths](property_paths.html)
--   [GROUP BY and counting](group-by.html)
--   [SELECT expressions](select_expr.html)
--   [Sub-SELECT](sub-select.html)
--   [Negation](negation.html)
+- [Frequently Asked Questions](faq.html)
+- [ARQ Support](support.html)
+- Application [javadoc](/documentation/javadoc/arq/index.html)
+- [Command line utilities](cmds.html)
+- [Querying remote SPARQL services](sparql-remote.html)
+  - [HTTP Authentication for ARQ](http-auth.html)
+- [Logging](logging.html)
+- [Explaining queries](explain.html)
+- [Tutorial: manipulating SPARQL using ARQ](manipulating_sparql_using_arq.html)
+- [Basic federated query (`SERVICE`)](service.html)
+- [Property paths](property_paths.html)
+- [GROUP BY and counting](group-by.html)
+- [SELECT expressions](select_expr.html)
+- [Sub-SELECT](sub-select.html)
+- [Negation](negation.html)
 
 Features of ARQ that are legal SPARQL syntax
 
--   [Conditions in FILTERs](function_forms.html)
-
--   [Free text searches](text-query.html)
--   [Accessing lists](rdf_lists.html) (RDF collections)
--   [Extension mechanisms](extension.html)
-    -   [Custom Expression Functions](extension.html#valueFunctions)
-    -   [Property Functions](extension.html#property-functions)
--   Library
-    -   [Expression function library](library-function.html)
-    -   [Property function library](library-propfunc.html)
--   [Writing SPARQL functions](writing_functions.html)
--   [Writing SPARQL functions in JavaScript](javascript-functions.html)
--   [Constructing queries programmatically](programmatic.html)
--   [Parameterized query strings](parameterized-sparql-strings.html)
--   [ARQ and the SPARQL algebra](algebra.html)
--   [Extending ARQ query execution and accessing different storage implementations](arq-query-eval.html)
--   [Custom aggregates](custom_aggregates.html)
+- [Conditions in FILTERs](function_forms.html)
+
+- [Free text searches](text-query.html)
+- [Accessing lists](rdf_lists.html) (RDF collections)
+- [Extension mechanisms](extension.html)
+  - [Custom Expression Functions](extension.html#valueFunctions)
+  - [Property Functions](extension.html#property-functions)
+- Library
+  - [Expression function library](library-function.html)
+  - [Property function library](library-propfunc.html)
+- [Writing SPARQL functions](writing_functions.html)
+- [Writing SPARQL functions in JavaScript](javascript-functions.html)
+- [Constructing queries programmatically](programmatic.html)
+- [Parameterized query strings](parameterized-sparql-strings.html)
+- [ARQ and the SPARQL algebra](algebra.html)
+- [Extending ARQ query execution and accessing different storage implementations](arq-query-eval.html)
+- [Custom aggregates](custom_aggregates.html)
 
 ## Extensions
 
 Feature of ARQ that go beyond SPARQL syntax. The default query
 language is standard SPARQL. These features require the query to be
 parsed with an explicit declaration of `Syntax.syntaxARQ`.
 
--   [RDF-star](https://w3c.github.io/rdf-star/)
--   Operators and functions
+- [RDF-star](https://w3c.github.io/rdf-star/)
+- Operators and functions
     `[MOD](https://www.w3.org/TR/xpath-functions/#func-numeric-mod)`
     and `[IDIV](https://www.w3.org/TR/xpath-functions/#func-numeric-integer-divide)` for modulus and integer division.
--   [LET variable assignment](assignment.html)
--   [Order results using a Collation](collation.html)
--   [Construct Quad](construct-quad.html)
--   [Generate JSON from SPARQL](generate-json-from-sparql.html)
+- [LET variable assignment](assignment.html)
+- [Order results using a Collation](collation.html)
+- [Construct Quad](construct-quad.html)
+- [Generate JSON from SPARQL](generate-json-from-sparql.html)
 
 ## Update
 
 ARQ supports the W3C standard SPARQL Update language.
 
--   [SPARQL Update](http://www.w3.org/TR/sparql11-update/)
--   [The ARQ SPARQL/Update API](update.html)
+- [SPARQL Update](http://www.w3.org/TR/sparql11-update/)
+- [The ARQ SPARQL/Update API](update.html)
 
 ## See Also
 
@@ -94,30 +94,29 @@ ARQ supports the W3C standard SPARQL Update language.
 
 ## W3C Documents
 
--   [SPARQL Query Language specification](http://www.w3.org/TR/sparql11-query/)
--   [SPARQL Query Results JSON Format](https://www.w3.org/TR/sparql11-results-json/)
--   [SPARQL Protocol](http://www.w3.org/TR/rdf-sparql-protocol/)
+- [SPARQL Query Language specification](http://www.w3.org/TR/sparql11-query/)
+- [SPARQL Query Results JSON Format](https://www.w3.org/TR/sparql11-results-json/)
+- [SPARQL Protocol](http://www.w3.org/TR/rdf-sparql-protocol/)
 
 ## Articles
 
 Articles and documentation elsewhere:
 
--   [Introducing SPARQL: Querying the Semantic Web](http://xml.com/lpt/a/2005/11/16/introducing-sparql-querying-semantic-web-tutorial.html)
+- [Introducing SPARQL: Querying the Semantic Web](http://xml.com/lpt/a/2005/11/16/introducing-sparql-querying-semantic-web-tutorial.html)
     ([xml.com](http://www.xml.com/) article by Leigh Dodds)
--   [Search RDF data with SPARQL](http://www.ibm.com/developerworks/xml/library/j-sparql/)
+- [Search RDF data with SPARQL](http://www.ibm.com/developerworks/xml/library/j-sparql/)
     (by Phil McCarthy) - article published on IBM developer works about
     SPARQL and Jena.
--   [SPARQL reference card](http://www.dajobe.org/2005/04-sparql/)
+- [SPARQL reference card](http://www.dajobe.org/2005/04-sparql/)
     (by [Dave Beckett](http://www.dajobe.org/))
--   [Parameterised Queries with SPARQL and ARQ](http://www.ldodds.com/blog/archives/000251.html)
+- [Parameterised Queries with SPARQL and ARQ](http://www.ldodds.com/blog/archives/000251.html)
     (by Leigh Dodds)
--   [Writing an ARQ Extension Function](http://www.ldodds.com/blog/archives/000252.html)
+- [Writing an ARQ Extension Function](http://www.ldodds.com/blog/archives/000252.html)
     (by Leigh Dodds)
 
 ## RDF Syntax Specifications
 
--   [Turtle](https://www.w3.org/TR/turtle/)
--   [N-Triples](https://www.w3.org/TR/n-triples)
--   [TriG](https://www.w3.org/TR/trig/)
--   [N-Quads](https://www.w3.org/TR/n-quads/)
-
+- [Turtle](https://www.w3.org/TR/turtle/)
+- [N-Triples](https://www.w3.org/TR/n-triples)
+- [TriG](https://www.w3.org/TR/trig/)
+- [N-Quads](https://www.w3.org/TR/n-quads/)

source/documentation/query/arq-query-eval.md

@@ -182,8 +182,8 @@ The steps from algebra generation to query evaluation are carried
 out when a query is executed via the `QueryExecution.execSelect` or
 other `QueryExecution` exec operation. It is possible to carry out
 storage-specific operations when the query execution is created. A
-query engine works in conjunction with a `QueryExecution` created
-by the `QueryExecutionFactory` to provide the evaluation of a query
+query engine works in conjunction with a `QueryExecution`
+to provide the evaluation of a query
 pattern. `QueryExecutionBase` provides all the machinery for the
 different result types and does not need to be modified by
 extensions to query execution.
@@ -490,8 +490,7 @@ While it is possible to replace the entire process of query
 evaluation, this is a substantial endeavour. `QueryExecutionBase`
 provides the machinery for result presentation (`SELECT`,
 `CONSTRUCT`, `DESCRIBE`, `ASK`), leaving the work of pattern
-evaluation to the custom query engine. `QueryExecutionFactory`
-assumes that `QueryExecutionBase` will be used.
+evaluation to the custom query engine.
 
 ## Algebra Extensions
 

source/documentation/query/construct-quad.md

@@ -119,7 +119,7 @@ previous sections, e.g.
 
     String queryString = " CONSTRUCT { GRAPH <http://example/ns#g1> {?s ?p ?o} } WHERE {?s ?p ?o}" ;
     Query query = QueryFactory.create(queryString, Syntax.syntaxARQ);
-    try ( QueryExecution qExec = QueryExecutionFactory.sparqlService(serviceQuery, query) ) { // serviceQuery is the URL of the remote service
+    try ( QueryExecution qExec = QueryExecution.service(serviceQuery).query(query).build() ) { // serviceQuery is the URL of the remote service
         Iterator<Quad> result = qExec.execConstructQuads();
         ...
     }

source/documentation/query/explain.md

@@ -74,8 +74,7 @@ globally:
 and it may also be set on an individual query execution using its local
 context.
 
-     try(QueryExecution qExec = QueryExecutionFactory.create(...)) {
-         qExec.getContext().set(ARQ.symLogExec, Explain.InfoLevel.ALL) ;
+     try(QueryExecution qExec = QueryExecution.create() ... .set(ARQ.symLogExec, Explain.InfoLevel.ALL).build() ) {
          ResultSet rs = qExec.execSelect() ;
          ...
      }

source/documentation/query/logging.md

@@ -96,8 +96,7 @@ globally:
 and it may also be set on an individual query execution using its local
 context.
 
-     try(QueryExecution qExec = QueryExecutionFactory.create(...)) {
-        qExec.getContext().set(ARQ.symLogExec, Explain.InfoLevel.ALL) ;
+     try(QueryExecution qExec = QueryExecution.create()... .set(ARQ.symLogExec, Explain.InfoLevel.ALL).build) {
         ...
      }
 

source/documentation/query/sparql-remote.md

@@ -5,8 +5,7 @@ title: ARQ - Querying Remote SPARQL Services
 SPARQL is a
 [query language](http://www.w3.org/TR/sparql11-query/) and a
 [remote access protocol](http://www.w3.org/2001/sw/DataAccess/proto-wd/).
-The remote access protocol can be used with plain HTTP or over
-[SOAP](http://www.w3.org/TR/soap12-part0/).
+The remote access protocol runs over HTTP.
 
 See [Fuseki](../fuseki2/index.html) for an implementation of the
 SPARQL protocol over HTTP. Fuseki uses ARQ to provide SPARQL 
@@ -16,12 +15,9 @@ ARQ includes a query engine capable of using the HTTP version.
 
 ## From your application
 
-The `QueryExecutionFactory` has methods for creating a
-`QueryExecution` object for remote use.
-`QueryExecutionFactory.sparqlService`
-
-These methods build a query execution object that uses the query
-engine in `org.apache.jena.sparql.engine.http`.
+The `QueryExecutionHTTP` has methods for creating a
+`QueryExecution` object for remote use. There are various
+HTTP specific settings; the default should work in most cases.
 
 The remote request is made when the `execSelect`, `execConstruct`,
 `execDescribe` or `execAsk` method is called.
@@ -43,7 +39,7 @@ sending.
 
 ## Authentication
 
-ARQ provides a flexible API for authenticating against remote services, see the [HTTP Authentication](http-auth.html) documentation for more details.
+ARQ provides a flexible API for authenticating against remote services, see the [HTTP Authentication](../sparql-apis/http-auth.html) documentation for more details.
 
 ## Firewalls and Proxies