D-Net

refactoring for proper publishing on JRR

Removed deprecated method

Logging the query

Due to r53449 we do not need the <> anymore when querying in the provenance graph

CRM.E29_Design_or_Procedure should always win as specific type (George maps Standard as Dataset and Design_or_Procedure but we want to see them among the Standards, not the datasets).

Fixes https://support.d4science.org/issues/11240#note-27: namespace dnet should not be used. The full namespace URL must be used when adding triples, otherwise it will be just a string, not a real name under the namespace as expected.

Fixes #11240#note-21: changed names of provenance graph and properties to be URLs instead of plain strings.

Let's return blank string upon error instead of throwing exception

Fixed web param name and ignoring webmvc test

Added new timeout parameter for anytime query

removed old commented code

Removed/deprecated unused methods

New methods to get subjects with pagination given a datasource API

Do not log 200 status

Bypassing Query and QueryEngineFactory, otherwise we cannot use the inference rules

Need to use inference rules also in /subjectsWithType method

Loggin queries that returned 504 GatewayTimeout

Let\s check if we do not get the following warning at client side by setting the response status in void GET methods that write directly on the output stream. The warning is: 'org.springframework.http.converter.json.MappingJackson2HttpMessageConverter- Failed to evaluate serialization for type [void]: java.lang.IllegalStateException: Failed to instantiate standard serializer (of type com.fasterxml.jackson.databind.ser.std.NullSerializer): Class com.fasterxml.jackson.databind.ser.BasicSerializerFactory can not access a member of class com.fasterxml.jackson.databind.ser.std.NullSerializer with modifiers "private"'

better error logging

handle httpstatus properly

Added TODO to remember in the near future about the error handling

Let's not log all queries, just the template name

crm prefix was unknown, let's use the full URI names fro the types we want to skip

Let's exclude E55_Type and E41_Appellation, not all entities whose type is not in the parthenos namespace

I think we must use an InfModel to process the rdf before registering it

Extract the rdf block from the record submitted for registration

No need to go through jena Model before delivering the response in the output stream

No need to log the endpoint every time

Can't use jena Query because does not support inference rule, can't use jena HttpEngine because it does not support long queryif we do not use Query: hence let's query with handmade post request to the sparql endpoint.

Getting unexpected 406 because of wrong sparql query..some debug logs might help

ByPass QueryBuilder, otherwise the virtuoso pragma are not parsable

Playing with inference rules on the remote sparql endpoint

Additional methods needed by the JRR publishing workflow

For almost every graph we used to return also "concept URLs" like "http://parthenos.d4science.org/handle/Parthenos/REG/Concept/datasettype/metadata"...let's try to avoid them skipping non URL resources and resources whose type is not in the parthenos namespace.

Back with no inference, otherwise we are passing all triples in CIDOC-CRM, DIG and PE, which is not what we want.

Add inferred info after getting sparql result.

Back to simple construct

using lambdas

Let's try using a VirtGraph

We should be able to use DEFINE if we use Virtuoso specific classes, see https://www.openlinksw.com/vos/main/Main/VirtJenaSPARQLExample12

it seems 406 really depends on the DEFINE construct to use inf rules...

Test: 406 error if I use the inference rules?

Use inference rules

Let's try to get only the triples where the known resource is subject

Let's throw exceptions!

Serialize in XML RDF PLAIN and not ABBREV

cleanup

DESCRIBE query does not work: we do not know what Virtuoso can return. Now we explicitely ask for all triples where a resource is involved as subject or object

API that read from Virtuoso

logs

Better close the Jena Model to ensure resources are released.

Fixed virtuoso drop and added test

getting ready to use the GCube Parthenos Registry

Log errors

More logs

API for storing on virtuoso

keep playing with virtuoso

JobNodes to work with Virtuoso

reformat code

added comment

VirtuosoClient and some tests assuming there is a local virtuoso server (hence ignored)

First tests with Virtuoso.