Refactor out SPIN

[blcham]

STEPS:

• check first if it is not possible to upgrade to SHACL while having SPIN as well
• if not create tests for all usecases where SPIN functionalities are used (e.g. RDF function definition)
• try to get rid of the implementation
• upgrade Jena and JOPA to newest version -- should also upgrade JSONLD library to https://github.com/filip26/titanium-json-ld

[blcham]

Related issues #43 #44

[blcham]

Additional notes:

• SHACL is the replacement for SPIN that we should use
• The relevant library that needs to be upgraded is in s-pipes core:

            <groupId>org.topbraid</groupId>
            <artifactId>shacl</artifactId>
            <version>1.0.1</version>
  

  I believe this is the last version of SHACL library that still contains the SPIN API. Here is also migration guide from SPIN to SHACL -- https://spinrdf.org/spin-shacl.html.

[blcham]

Next steps:

• Choose SHACL library to replace SPIN (jena-shacl vs. topbraid-shacl) -- here is comparison
  • we should use jena-shacl if possible, as it is not vendor-locked. For now, I do not see any specific topbraid-shacl feature that we need.
• modify/extend Spin integration test to SHACLIntegrationTest to test needed features. Follow the migration guide. We need to:
  • migrate all SPARQL functions written in Java from SPIN to SHACL (e.g. AddDays.java) and make test to prove they work in a SPARQL query
  • be able to define a specific function in RDF and then call it in SPARQL query
    • see "User-Defined (SPARQL) Functions" section in https://spinrdf.org/spin-shacl.html
  • migrate doc/examples to use SHACL instead of SPIN (note we can but not have to support loading it through SPIN namespace, i.e. sp:Select, sp:text etc.)

[blcham]

@palagdan let's start implementation without upgrading SHACL library:

migrate all SPARQL functions written in Java from SPIN to SHACL (e.g. AddDays.java) and make test to prove they work in a SPARQL query

STEPS:

• make new test in

  s-pipes/s-pipes-core/src/test/java/cz/cvut/spin/SpinIntegrationTest.java

  Line 19 in 038b350

  public class SpinIntegrationTest {

  to prove that function in AddDays.java works in a query
• reimplement functions using SHACL API
• reimplement test in SHACLIntegrationTest

I created initial PR -- #251

[palagdan]

@blcham
I tested the AddDays function you provided:

@Test
    public void executeSPINQueryWithCustomJavaFunction() {
        PipelineFactory pipelineFactory = new PipelineFactory();

        String queryString = """
                PREFIX kbss-timef: <http://onto.fel.cvut.cz/ontologies/lib/function/time/>
                PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
                SELECT ?nextDay 
                WHERE {
                  BIND(kbss-timef:add-days("2022-01-01"^^xsd:date, 1) AS ?nextDay)
                }
                """;
        Model model = ModelFactory.createDefaultModel();

        Query query = QueryFactory.create(queryString);


        QueryExecution qexec = QueryExecutionFactory.create(query, model);
        ResultSet results = qexec.execSelect();

        if (results.hasNext()) {
            QuerySolution soln = results.nextSolution();
            assertEquals(soln.getLiteral("nextDay").getString(), "2022-01-02");
        }
    }

The test works fine. PipelineFactory registers all S-PIPES modules and functions.

However, I’m unsure how to reimplement functions like AddDays using SHACL because there is no available documentation on how to use the SHACL API.

Additionally, why should AddDays extend the SPIN AbstractFunction class? Since SPIN is designed for constraints and AddDays is a function that produces a Date output.