Update feedback:
Derby home setting is not necessary when setting the SIS_DATA variable.
Hence this is the cleaned up startup sequence in the docker entrypoint.sh:
# SiS_DATA set in docker-compose.yaml
export SIS_HOME=${SIS_DATA}/..
export START=`echo ${JAVA_HOME}/bin/java $JAVA_OPTIONS -classpath
${SIS_HOME}/lib/:"${FUSEKI_DIR}/${FUSEKI_JAR}":${SIS_HOME}/lib/derby-10.14.2.0.jar
org.apache.jena.fuseki.geosparql.Main "$@"`
echo ${START}
exec ${START}
Op vr 4 feb. 2022 om 09:54 schreef Erik Bijsterbosch <
e.bijsterbo...@gmail.com>:
>
> We successfully loaded two demo sets with CRS wgs84 and CRS 27700.
> So the geodetic EPSG dataset is used well.
> The problem must be in our srs uri's then and we will investigate our
> datasets and etl/minting on the schema's used.
>
> Attaching to fuseki
> fuseki | /fuseki/databases/SIS/apache-sis-1.1/data/
> fuseki | /opt/java-minimal/bin/java -Xmx24g -Xms24g
> -Dderby.system.home=/fuseki/databases/SIS/apache-sis-1.1/data/Databases
> -classpath
> /fuseki/databases/SIS/apache-sis-1.1/data/sis-embedded-data-1.1.jar:/fuseki/jena-fuseki-geosparql-4.4.0.jar
> org.apache.jena.fuseki.geosparql.Main -t /fuseki/databases/DB2-5 --tdb2
> --rdf_file /fuseki/store/geosparql_test.rdf --dataset dst
> --default_geometry --inference
> fuseki | WARNING: sun.reflect.Reflection.getCallerClass is not
> supported. This will impact performance.
> fuseki | [2022-02-04 08:59:49] INFO Main :: Arguments
> Received: [-t, /fuseki/databases/DB2-5, --tdb2, --rdf_file,
> /fuseki/store/geosparql_test.rdf, --dataset, dst, --default_geometry,
> --inference]
> fuseki | [2022-02-04 08:59:49] INFO DatasetOperations :: Server
> Configuration: port=3030, datsetName=dst, loopbackOnly=true,
> updateAllowed=false, inference=true, applyDefaultGeometry=true,
> validateGeometryLiteral=false, convertGeoPredicates=false,
> removeGeoPredicates=false, queryRewrite=true,
> tdbFile=/fuseki/databases/DB2-5,
> fileGraphFormats=[FileGraphFormat{rdfFile=/fuseki/store/geosparql_test.rdf,
> graphName=, rdfFormat=Turtle/pretty}], fileGraphDelimiters=[],
> indexEnabled=true, indexSizes=[-1, -1, -1], indexExpiries=[5000, 5000,
> 5000], spatialIndexFile=null, tdb2=true, help=false
> fuseki | [2022-02-04 08:59:49] INFO DatasetOperations :: TDB Dataset:
> /fuseki/databases/DB2-5, TDB2: true
> fuseki | [2022-02-04 08:59:50] INFO DatasetOperations :: Reading RDF -
> Started - File: /fuseki/store/geosparql_test.rdf, Graph Name: , RDF Format:
> Turtle/pretty
> fuseki | [2022-02-04 08:59:51] INFO DatasetOperations :: Reading RDF -
> Completed - File: /fuseki/store/geosparql_test.rdf, Graph Name: , RDF
> Format: Turtle/pretty
> fuseki | [2022-02-04 08:59:51] INFO GeoSPARQLOperations :: Applying
> hasDefaultGeometry - Completed
> fuseki | [2022-02-04 08:59:51] INFO GeoSPARQLOperations :: Applying
> GeoSPARQL Schema - Started
> fuseki | [2022-02-04 08:59:51] INFO GeoSPARQLOperations :: GeoSPARQL
> schema applied to graph: default
> fuseki | [2022-02-04 08:59:51] INFO GeoSPARQLOperations :: Applying
> GeoSPARQL Schema - Completed
> fuseki | [2022-02-04 08:59:51] INFO GeoSPARQLOperations :: Find Mode
> SRS - Started
> fuseki | [2022-02-04 08:59:51] INFO GeoSPARQLOperations :: Find Mode
> SRS - Completed
> fuseki | [2022-02-04 08:59:51] INFO SpatialIndex ::
> Feature-hasGeometry-Geometry statements found.
> fuseki | [2022-02-04 08:59:51] INFO SpatialIndex :: Saving Spatial
> Index - Started: /fuseki/databases/DB2-5/spatial.index
> fuseki | [2022-02-04 08:59:51] INFO SpatialIndex :: Saving Spatial
> Index - Completed: /fuseki/databases/DB2-5/spatial.index
> fuseki | [2022-02-04 08:59:51] INFO GeosparqlServer :: GeoSPARQL
> Server: Running - Port: 3030, Dataset: /dst, Loopback Only: true, Allow
> Update: false
> fuseki | [2022-02-04 08:59:51] INFO Server :: Start Fuseki
> (http=3030)
>
> Op do 3 feb. 2022 om 19:48 schreef Erik Bijsterbosch <
> e.bijsterbo...@gmail.com>:
>
>> The work around from https://sis.apache.org/javafx.html
>>
>> Op do 3 feb. 2022 om 19:46 schreef Erik Bijsterbosch <
>> e.bijsterbo...@gmail.com>:
>>
>>> Hi Andy,
>>>
>>> We advanced a few steps but now we're having trouble using the (full)
>>> geodetic EPSG dataset.
>>>
>>> $ docker-compose stop fuseki; docker-compose rm -f fuseki;
>>> docker-compose up fuseki
>>> Stopping fuseki ... done
>>> Going to remove fuseki
>>> Removing fuseki ... done
>>> Creating fuseki ... done
>>> Attaching to fuseki
>>> fuseki | /opt/java-minimal/bin/java -Xmx24g -Xms24g
>>> -Dderby.system.home=/fuseki/databases/SIS/apache-sis-1.1/data/Databases
>>> -classpath
>>> /fuseki/databases/SIS/apache-sis-1.1/lib/sis-referencing-1.1.jar:/fuseki/jena-fuseki-geosparql-4.4.0.jar
>>> org.apache.jena.fuseki.geosparql.Main -t /fuseki/databases/DB2-4 --tdb2
>>> --rdf_file /fuseki/store/ligplaats.trig --dataset dst --inference --validate
>>> fuseki | WARNING: sun.reflect.Reflection.getCallerClass is not
>>> supported. This will impact performance.
>>> fuseki | [2022-02-03 19:15:18] INFO Main :: Arguments
>>> Received: [-t, /fuseki/databases/DB2-4, --tdb2, --rdf_file,
>>> /fuseki/store/ligplaats.trig, --dataset, dst, --inference, --validate]
>>> fuseki | [2022-02-03 19:15:18] INFO DatasetOperations :: Server
>>> Configuration: port=3030, datsetName=dst, loopbackOnly=true,
>>> updateAllowed=false, inference=true, applyDefaultGeometry=false,
>>> validateGeometryLiteral=true, convertGeoPredicates=false,
>>> removeGeoPredicates=false, queryRewrite=true,
>>> tdbFile=/fuseki/databases/DB2-4,
>>> fileGraphFormats=[FileGraphFormat{rdfFile=/fuseki/store/ligplaats.trig,
>>> graphName=, rdfFormat=Turtle/pretty}], fileGraphDelimiters=[],
>>> indexEnabled=true, indexSizes=[-1, -1, -1], indexExpiries=[5000, 5000,
>>> 5000], spatialIndexFile=null, tdb2=true, help=false
>>> fuseki | [2022-02-03 19:15:18] INFO DatasetOperations :: TDB
>>> Dataset: /fuseki/databases/DB2-4, TDB2: true
>>> fuseki | [2022-02-03 19:15:19] WARN system :: The
>>> “SIS_DATA” environment variable is not set.
>>> fuseki | [2022-02-03 19:15:19] INFO DatasetOperations :: Reading RDF
>>> - Started - File: /fuseki/store/ligplaats.trig, Graph Name: , RDF Format:
>>> Turtle/pretty
>>> fuseki | [2022-02-03 19:15:20] WARN SRSRegistry :: SRS URI not
>>> recognised so operation results may not be correct or accurate:
>>> http://www.opengis.net/def/crs/EPSG/0/28992 - Unrecognised SRS URI
>>> code: http://www.opengis.net/def/crs/EPSG/0/28992 - No
>>> ‘CoordinateReferenceSystem’ object found for code “28992”. However only a
>>> subset of the EPSG geodetic dataset has been queried. See
>>> http://sis.apache.org/epsg.html for instruction about how to install
>>> the full EPSG database.
>>> fuseki | [2022-02-03 19:15:27] INFO DatasetOperations :: Reading RDF
>>> - Completed - File: /fuseki/store/ligplaats.trig, Graph Name: , RDF Format:
>>> Turtle/pretty
>>> fuseki | [2022-02-03 19:15:27] INFO GeoSPARQLOperations :: Applying
>>> GeoSPARQL Schema - Started
>>> fuseki | [2022-02-03 19:15:32] INFO GeoSPARQLOperations :: GeoSPARQL
>>> schema applied to graph: default
>>> fuseki | [2022-02-03 19:15:32] INFO GeoSPARQLOperations :: Applying
>>> GeoSPARQL Schema - Completed
>>> fuseki | [2022-02-03 19:15:32] INFO GeoSPARQLOperations :: Find Mode
>>> SRS - Started
>>> fuseki | [2022-02-03 19:15:32] INFO GeoSPARQLOperations :: Find Mode
>>> SRS - Completed
>>> fuseki | [2022-02-03 19:15:32] ERROR Main :: GeoSPARQL
>>> Server: Exiting - No SRS found. Check '
>>> http://www.opengis.net/ont/geosparql#hasSerialization' or '
>>> http://www.w3.org/2003/01/geo/wgs84_pos#lat'/'http://www.w3.org/2003/01/geo/wgs84_pos#lon'
>>> predicates are present in the source data. Hint: Inferencing with GeoSPARQL
>>> schema may be required.: dst
>>>
>>> The was created manually with the CLI with the work around from :
>>>
>>>
>>> - cd /fuseki/databases/SIS/apache-sis-1.1/data
>>> - rm -rf Databases
>>> - wget
>>>
>>> https://repo1.maven.org/maven2/org/apache/sis/non-free/sis-embedded-data/1.1/sis-embedded-data-1.1.jar
>>> - unzip sis-embedded-data-1.1.jar SIS_DATA/Databases/*
>>> - mv SIS_DATA/Databases .
>>> - rmdir SIS_DATA
>>> - cd ..
>>> - sis crs EPSG:28992
>>>
>>> output:
>>>
>>> ProjectedCRS["Amersfoort / RD New",
>>> BaseGeodCRS["Amersfoort",
>>> Datum["Amersfoort",
>>> Ellipsoid["Bessel 1841", 6377397.155, 299.1528128]],
>>> Unit["degree", 0.017453292519943295]],
>>> Conversion["RD New",
>>> Method["Oblique Stereographic"],
>>> Parameter["Latitude of natural origin", 52.15616055555556],
>>> Parameter["Longitude of natural origin", 5.387638888888891],
>>> Parameter["Scale factor at natural origin", 0.9999079],
>>> Parameter["False easting", 155000.0],
>>> Parameter["False northing", 463000.0]],
>>> CS[Cartesian, 2],
>>> Axis["Easting (X)", east],
>>> Axis["Northing (Y)", north],
>>> Unit["metre", 1],
>>> Scope["Large and medium scale topographic mapping and engineering
>>> survey."],
>>> Area["Netherlands - onshore, including Waddenzee, Dutch Wadden Islands
>>> and 12-mile offshore coastal zone."],
>>> BBox[50.75, 3.20, 53.70, 7.22],
>>> Id["EPSG", 28992, "9.9.1", URI["urn:ogc:def:crs:EPSG:9.9.1:28992"]],
>>> Remark["Replaces Amersfoort / RD Old (code 28991)."]]
>>>
>>>
>>>
>>>
>>> Op wo 2 feb. 2022 om 12:11 schreef Andy Seaborne <a...@apache.org>:
>>>
>>>>
>>>>
>>>> On 02/02/2022 10:17, Erik Bijsterbosch wrote:
>>>> > Hi Andy,
>>>> >
>>>> > Good to know that the code loops through all the (named) graphs.
>>>> > I noticed later in the logs that fuseki was still busy with the next
>>>> > (named) graph, apparently.
>>>> > It seems that that attempt failed on the type of geometry we have in
>>>> this
>>>> > graph:
>>>> >
>>>> > [2022-02-02 09:32:27] WARN system :: The “SIS_DATA”
>>>> environment
>>>> > variable is not set.
>>>> > [2022-02-02 09:32:28] WARN system :: The “SIS_DATA”
>>>> environment
>>>> > variable is not set.
>>>> > Exception in thread "main"
>>>> > org.apache.jena.dboe.transaction.txn.TransactionException: Write
>>>> > transaction with no commit() or abort() before end() - forced abort
>>>> > at
>>>> >
>>>> org.apache.jena.dboe.transaction.txn.Transaction.end(Transaction.java:203)
>>>> > at
>>>> >
>>>> org.apache.jena.dboe.transaction.txn.TransactionalBase._end(TransactionalBase.java:262)
>>>> > at
>>>> >
>>>> org.apache.jena.dboe.transaction.txn.TransactionalBase.end(TransactionalBase.java:168)
>>>> > at
>>>> >
>>>> org.apache.jena.dboe.storage.system.DatasetGraphStorage.end(DatasetGraphStorage.java:73)
>>>> > at
>>>> >
>>>> org.apache.jena.sparql.core.DatasetGraphWrapper.end(DatasetGraphWrapper.java:284)
>>>> > at
>>>> org.apache.jena.sparql.core.DatasetImpl.end(DatasetImpl.java:162)
>>>> > at
>>>> >
>>>> org.apache.jena.geosparql.configuration.GeoSPARQLOperations.applyInferencing(GeoSPARQLOperations.java:297)
>>>> > at
>>>> >
>>>> org.apache.jena.geosparql.configuration.GeoSPARQLOperations.applyInferencing(GeoSPARQLOperations.java:264)
>>>> > at
>>>> >
>>>> org.apache.jena.fuseki.geosparql.DatasetOperations.setup(DatasetOperations.java:83)
>>>> > at org.apache.jena.fuseki.geosparql.Main.main(Main.java:64)
>>>>
>>>> Should be a log line: "Inferencing Error: ..." as well or there is a
>>>> java Throwable/Error happening e.g. OutOfMemoryError.
>>>>
>>>> >
>>>> > For that we'll checkout the recommendations here first:
>>>> > https://sis.apache.org/epsg.html
>>>> >
>>>> >
>>>> > Op wo 2 feb. 2022 om 09:33 schreef Andy Seaborne <a...@apache.org>:
>>>> >
>>>> >>
>>>> >>
>>>> >> On 01/02/2022 17:13, Erik Bijsterbosch wrote:
>>>> >>> Hi all,
>>>> >>>
>>>> >>> I created a new jena tdb2 database and loaded it with 256 million
>>>> triples
>>>> >>> in a named graph, using a fuseki2/tdb2 4.3.2 docker setup.
>>>> >>> The data also consist of geometries so I built a new docker image
>>>> based
>>>> >> on
>>>> >>> jena-fuseki-geosparql 4.3.2
>>>> >>> When I bring up the new fuseki container it seems I can't address
>>>> the
>>>> >> named
>>>> >>> graph reusing the tdb2 database, it searches through the default
>>>> graph.
>>>> >>> According to the --help graph names can only be provided when
>>>> loading
>>>> >> from
>>>> >>> files or is there another way?
>>>> >>
>>>> >>
>>>> >> Hi Erik,
>>>> >>
>>>> >>> fuseki | [2022-02-01 17:08:15] INFO GeoSPARQLOperations ::
>>>> GeoSPARQL
>>>> >>> schema not applied to empty graph: default
>>>> >>
>>>> >> That message is for the attempt the default graph but it does not
>>>> mean
>>>> >> it is ignoring the named graphs. The code loops on the named graphs
>>>> as
>>>> >> well.
>>>> >>
>>>> >>
>>>> >>
>>>> https://github.com/apache/jena/blob/main/jena-geosparql/src/main/java/org/apache/jena/geosparql/configuration/GeoSPARQLOperations.java#L269
>>>> >>
>>>> >> Is that what you mean by "can't address the named graph"?
>>>> >>
>>>> >> Or from a SPARQL query you can't get expected results?
>>>> >>
>>>> >> Andy
>>>> >>
>>>> >
>>>>
>>>
